My first revelation while watching Cave of Forgotten Dreams (IFC Films), Werner Herzog's three-dimensional documentary about 30,000-year-old paintings, seemed face-palm silly a moment later: Our caveman ancestors really knew how to draw. Well of course they did. Prehistoric man wasn't skipping through the glacial landscape and scrawling on rocks like a child. He was an adult, just like you and me—and had an adult's capacity for graceful lines and shading. With a bit of homo savvy, he even appears to have figured out how to depict motion in his art. The film shows us, at one point, an eight-legged bison painted on limestone, as if the animal were posed in sequential frames of action. A sort of "proto-cinema," Herzog calls it.

Herzog is right that the setting for his film—the magnificent Chauvet cave in southern France—feels like an ancient movie theater. The paintings are situated in a dark chamber draped with calcite curtains and lit up with flickering beams from the camera crew. Framed by stalagmites, the caveman drawings seem as if they're being projected onto the walls via flashlight. (Some are overlaid on even more ancient marks—the four-lined scratches of cave bears.) After spending 90 minutes in this environment, minus some time for talking-head interviews and the obligatory epilogue about albino crocodiles, I re-emerged into the sunlight a little shaken. And quite moved: Cave of Forgotten Dreams is a Herzogian masterpiece—a ponderous and nauseating theme-park ride, but one that unfolds as a probing essay on the history of art.

That Herzog shot the film entirely in 3-D seems like a joke at first: the most primitive images in human history, brought to you with the latest high-tech Hollywood gadgets! But there's more going on here than a contrast of Neanderthal and Na'vi. I've never seen the stereo effect deployed with such purpose and beauty. The double-lens camera evokes depth at multiple scales, plunging us first into a claustrophobic, underground space and then across the rippled limestone walls of its interior. Herzog treats the 3-D camera as a metaphor, too—a machine that fuses art and science, the twin tracks of human innovation, into a single, voluminous whole. That's not to say the stereography is perfect; in a few scenes, it comes off as a stomach-churning, washed-out mess. But in most of the film, the 3-D is beyond immersive: It reveals facets of the paintings that would otherwise be invisible and conveys a deeper truth about how we make images and perceive them.

"Once you see the cave with your own eyes, you realize it had to be filmed in 3-D," Herzog told the Los Angeles Times last year. Indeed, the movie demonstrates how the prehistoric artists used rocky undulations to create their own sort of depth effect. A horse's foreleg painted on a swell seems to possess a bulging quadriceps; a bison's head drawn on the rounded surface of a stalactite envelops a picture of a woman's genitals. Try closing one eye as you watch: All the subtle bends and curves fall flat into the frame. Even Roger Ebert, the nation's most intractable 3-D curmudgeon, acknowledged that way down in the Chauvet cave, at least, the Hollywood gimmick is appropriate and useful.

This latter concession comes from a man whose rants against 3-D have appealed more than once to our ancient ancestors on the savannah—folks, he says, who never evolved the ability to don polarized specs. When they spied an advancing bear or boulder, their instinct would have been to leap aside or run away. Not to sit in place like a bunch of 21^st-century couch potatoes. We just aren't made to watch 3-D movies.

OK, so there might not have been so much adaptive value, back then, in reading binocular depth cues off a level surface. But what business did these cavemen have drawing a bison in full gallop or the topology of a horse's flesh? Wasn't there some better use for their blossoming gray matter? The heroes of Cave of Forgotten Dreams are those prehistoric draftsmen whose desire to make pictures was just as silly and maladaptive and profound as our own. They fussed over lines and texture and the curving canvas of the walls around them; we fiddle with battery-powered flashlights and stereographic cameras. Near the end of Herzog's spelunking expedition, he lingers on an image of an ancient stalagmite and stalactite that stretch toward each other but don't quite meet; between them is a teardrop of empty space. It's the most striking image in the film—a symbol of the artists at Chauvet, then and now, reaching out across the millenniums.

It helps that Herzog chose the ideal environment for shooting in stereo. After watching the My Bloody Valentine remake in 2009, it occurred to me the medium was most at home in caves and mineshafts. When you're underground, the well-documented annoyances of 3-D—dim lighting, washed-out colors, a claustrophobic shrinking of scale—imbue the scene with atmosphere. A dim and splotchy image looks terrible when viewed flat, just a jumble of shadows. But put on the glasses and those shadows coalesce and inflate; the darkness rises off the screen like a mist. That's a lovely backdrop for a killer dragging his pickaxe through the mines, but it's just as useful at Chauvet, where we're always peering over Herzog's shoulder through a sea of black.

When the film crew retreats to the surface, the 3-D begins to flounder. The wooded hills around the cave look drab and dusky, as if a storm were always about to break. And the puppet-theater effect—that troublesome way in which 3-D landscapes come to resemble living dioramas—sabotages Herzog's efforts at majestic aerial shots. One outdoor sequence deserves special reproach: a jerky hike up the mountainside, filmed by hand with an upside-down camera. I'm not sure what the director was trying to conjure with this 3-D circus shot, other than my breakfast. (Another awkwardness: The subtitles. The question of where to place text in a 3-D film is more vexing than you might think. Should the words be all the way in the foreground, with the action unfolding behind them? Or at the level of the screen? When something moves in front of a subtitle, should the letters still show through? And so forth.)

Maybe some of these difficulties explain Herzog's avowed antipathy toward 3-D. In September, he swore off the medium altogether. ("I've never used the process in the 58 films I made before and I have no plans to do it ever again.") That's a shame: Despite some glitches, Cave of Forgotten Dreams comes off as a triumph for stereo cinema. Or more than a triumph: I'm pretty sure it's one of the best 3-D movies ever made.