The South African, whose only victory on American soil came in last year's U.S. Open, shot a 4-under-par 68 in the third round of the BellSouth Classic to take a two-stroke lead over Mickelson.
Goosen launched a streak of five birdies in six holes by sinking a 20-foot putt at No. 9, one of the toughest tests on the TPC at Sugarloaf. He signed for the lowest score of the day, one of just 10 players who broke into the 60s.
Three days of sunny skies and steady breezes turned the greens rock-hard, mimicking conditions that will be the norm at Augusta National next weekend.
Mickelson found out just how tricky those greens can be, four-putting the 13th to rekindle memories of a similar debacle at The Players Championship.
'If you get on the wrong side of the flag, anything can happen - no matter how good your short game is,' said Goosen, who knows a thing or two about missing short putts. 'I'm a little surprised he's not higher.'
Still, Mickelson was in contention for the 21st victory of his career, more than any active player except Tiger Woods.
Goosen had bogeys at 16 and 18, finishing with a 14-under 202. Mickelson was at 204 after shooting a third-round 71.
'The greens are very difficult,' Lefty said. 'I made countless 4- to 6-footers for par. Obviously, I missed one at 13, but I hit a lot of good shots. For the most part, I thought I played well.'
After making the turn with a two-stroke lead over Goosen, Mickelson found himself tied when he walked away from the par-5 10th.
Goosen birdied the hole, while Mickelson came up a club short with his second shot - winding up in the front bunker.
Mickelson chunked his sand wedge - barely clearing the lip of the bunker - and left the ensuing chip 12 feet from the flag. He missed the putt for just his third bogey of the tournament, knowing this was a hole where he should have done no worse that par.
Then came the meltdown at 13, the shortest par-4 on the course at 310 yards. Playing in the group ahead of Mickelson, Goosen came through with another birdie, leaving his tee shot just off the green, chipping to 19 feet and sinking the putt.
Mickelson drove onto the green for the second time in three days, but it did him no good. His first putt, downhill from about 50 feet away, stopped short and left a testy 3-footer.
The birdie attempt slid 6 feet past the hole, and the comebacker missed, too. Mickelson finally tapped in and walked off the green shaking his head.
Flash back to The Players two weeks ago. Mickelson knocked himself out of contention by five-putting the 10th green for a quadruple-bogey 8. The middle three putts were from 5 feet - and two of those were rush jobs.
Mickelson said this situation was different.
'I don't think this did nearly as much damage as the Players,' he said. 'People are going to make bogeys out there. I'm still right there atop the leaderboard. To be 12 under, I think that's some pretty good playing.'
Goosen has made a bunch of long putts - just as he did last year at the U.S. Open before his infamous 18-inch miss on the 72nd hole left him tied with Mark Brooks.
Goosen recovered to win an 18-hole playoff the following day, the biggest victory of his career.
The somber South African began his surge to the BellSouth lead at No. 9, a 465-yard hole that surrendered only 10 birdies all day. He sank a 25-footer for birdie at the 12th, then another 20-footer at 13.
'I'm pretty happy where I am,' Goosen said. 'I've not been playing well this week at all. But I've been putting great, and that's why I am where I am.'
Steve Elkington, who led after the first round and was tied with Mickelson heading into Saturday, struggled to a 73 in the difficult conditions.
The Australian was still in contention for his first victory since 1999, four strokes back at 206 in a tie with Mike Weir.
Thomas Bjorn, who entered the BellSouth hoping to improve his game for the Masters, shot a 69 and was alone in third at 205.
News, Notes and Numbers
*Colin Montgomerie had the second hole-in-one of the tournament, using an 8-iron to sink his tee shot on the 172-yard 16th.
*Jesper Parnevik made a hole-in-one Friday on the eighth, but not much has gone right for the Swede since then. He's 7-over since holing out, including a third-round 76 that knocked him out of contention.
*The most surprising player in the field? That's easy. Zach Johnson, a regular on the Hooters Tour, was at 208 - tied for eighth - playing in just his second PGA Tour event. Johnson had to qualify on Monday just to earn a spot in the field.
Full-field scores from the BellSouth Classic