It was the age of Spain’s Inquisition and its Age of Gold. King Felipe II, who ascended the throne in 1556, lost an “invincible” armada to the fleet of Protestant England, but he also built the breathtaking palace of El Escorial near Madrid. In swift succession, he married four wives from the four great royal houses of Europe — Portugal, England, France and Austria — and fathered seven children.

Yet the Hapsburg dynasty fizzled out just a century after Felipe’s death in 1598, dwindling into a line of sickly kings with ever fewer successors — and finally none at all. Five portraits and a bronze bust of the ill-fated family occupy the first room of “Masterpieces From the Prado,” a magnificent new exhibition at The National Museum of Western Art in Tokyo’s Ueno that has ransacked Madrid’s foremost artistic treasure house.

However, the works on display aren’t a record only of aristocratic decline, since they also tell of artistic ascendancy. Though impressive, the bust of Felipe II’s father, Carlos I, a clear-eyed warrior in an ornamental breastplate, has none of the impact of Diego Velazquez’s somber portrait of Felipe IV. This is unsparing in its representation of the king’s fine hair, fleshy lips and famously prognathous Hapsburg jaw.

Unlike Titian, an earlier painter-by-appointment to the Spanish court who switched to lush, allegorical treatments to satisfy his monarch’s whim, Velazquez retained his elegant, realistic style — even when faced with competition from Peter Paul Rubens, who arrived in Madrid in 1628 and promptly dished up a heroic equestrian portrait of lop-eyed Felipe.

Heroism and realism fight it out not only in the first portrait room, but throughout this wide-ranging exhibition — which will surely have visitors to the Prado standing fuming before walls stripped bare of their Titians and Tintorettos, their Goyas and El Grecos.

The large second gallery showcases Italian and Flemish works from the Spanish collection, and contrasting works by individual artists are hung side by side. Three celebrated mythological scenes by Rubens fill the far wall: “Diana the Huntress,” “The Rape of Europa” and “Saturn Devouring His Son.” The first two exhibit the rosy, rounded limbs that made “Rubenesque” the euphemism it is for describing fuller-figured women. The lean athletic hounds of Diana and the glint in the eye of the bull — the god Zeus in disguise — bearing Europa away across the waves belong to the Olympian world of gods at sport.

By contrast, “Saturn” stops you in your tracks with its ghastly depiction of the god who believed that by devouring his own children, he could avert a prophecy that he would be overthrown by his son. In this disturbing scene, the child shrieks in agony as Saturn’s teeth pull and rip its flesh. In a gory touch, the aging god’s beard and nose are dabbled with his child’s blood.

Bloody, too, are the red-rimmed eyes of Christ that look out at the viewer from a shadowy and muted scene by Titian, dated ca. 1560. Here, the contrast with its companion piece — the surviving fragment of a much larger canvas by the artist, painted in 1553 — is even more pronounced. The earlier work is a serene head-and-shoulders representation of the resurrected savior, clad in blue and luminous white.

Religious works are at the heart of this exhibition, and in them the tensions between the ideal and the real are most heightened — and most intriguing. With the Reformation and the emergence of Protestantism in Europe, the Catholic Church had been put on the defensive. The Spanish Inquisition was only the most notorious manifestation of a threatened institution battening down the hatches in a bid to preserve orthodoxy. A little later, toward the end of the 16th century, came the so-called Catholic or Counter Reformation in which a renewed Church turned away from instruments of torture and toward works of devotion to sustain its faithful.

The arts had a central role to play in projecting heroic images of the assailed-yet-triumphant Church, in propagating new or improved doctrines and in creating tender devotional images. This exhibition has striking examples of all three. There is Titian’s gaudy “Religion Rescued by Spain” (1572-75), in which a stout blonde maiden marches to the rescue of a fainting, near-naked woman (the Church), an overturned eucharistic chalice at her feet symbolizing the Protestant denial of the Catholic mass. This work must have delighted Felipe II by being not only spiritually triumphalist but patriotic, too — France and Spain were vying for supremacy as defenders of the Catholic Faith, and Felipe had awarded himself the title of “Most Christian King.”

Murillo’s saccharine “The Immaculate Conception of Aranjuez” pulls off a similar feat. The Immaculate Conception — the belief that the soul of the Virgin Mary was created sinless by God — emerged as a mainstay of Counter-Reformation Catholicism. Thus depicted, with a number of symbolic attributes (principally a crescent moon beneath her feet), Mary Immaculate became a poster-girl for the Catholic cause.

Perhaps the loveliest picture in the whole exhibition is Francisco de Zubaran’s “Agnus Dei (Lamb of God),” a gentle lamb bound for sacrifice. This was surely a comforting image for the faithful who had suffered a double assault from both Protestantism and the Inquisitorial machine of their own Church.

Yet orthodoxy is rarely as interesting as unorthodoxy — and El Greco (1541-1614) was as innovative stylistically as in his handling of his religious subject matter. Where did his strong, stark palette and angular yet fluid forms come from, so unlike anything else of their age? And why did he leave no imitators behind, barely a ripple of interest even, until admiration for his works revived at the close of the 19th century?

The three fine canvases displayed here — principally “The Holy Family with St. Anne and St. John,” whose principal women could be studied for hours — raise these questions and many more besides.

Other works, too, will leave you transfixed: the dignified, level look of “The Buffon don Sebastian de Morra” (1643-44), the dwarf and court jester of Felipe IV painted by Velazquez; Goya’s “The Parasol” (1777), as bright and gay as “The Colossus” (1808), by the same artist, is dark and disturbing.

The penultimate chamber of the gallery holds portraits of the Bourbons of France who succeeded to the Spanish throne on the demise of the Hapsburg line: handsome Felipe V and his wife Isabella Farnese, and their son Carlos III, a bright-eyed, periwigged boy. It was Carlos’ grandson, Ferdinand VII, who established the Prado in 1819 as the Royal Museum of Painting and Sculpture. Yet its collection seems most to reflect the spirit of the Hapsburgs who first brought it together.

Back in the first room, the full-length likeness of the last of the Hapsburg line, a ghost-faced Carlos II at age 10, gazes weakly into the stern face of his forbear, Felipe II, whose portrait hangs opposite. Carlos holds a silk handkerchief limply in his right hand, a floppy hat in his left; Felipe rests one fist on the pommel of his sword and runs a rosary through the fingers of the other.

Sword and rosary, silk and sobriety, Inquisition and Age of Gold: this magnificent exhibition captures it all.