The roars that normally echo through the Georgian pines were replaced by groans and sighs as some of golf's biggest names, including Phil Mickelson, failed to make it past the second round.
While most of the world's best golfers struggled to make par in the brutally tough conditions, the free-swinging Watson surged into contention for a second green jacket in three years.
The American produced a masterful display on the back nine to grab the outright lead at seven-under-par and hold a three-shot advantage over Australia's John Senden.
Another four players, including defending champion Adam Scott, were tied for third at three-under on a congested leaderboard.
The Australian battled to a 72 to join Denmark's Thomas Bjorn (68), Swede Jonas Blixt (71) and American Jordan Spieth (70), the last pair being among the record 24 rookies in the field.
"It wasn't exactly what I was looking for," Scott said. "But given everything, I'm absolutely satisfied with that."
The unflappable Fred Couples, the 1992 champion, finished with a 71 to join Jimmy Walker (72) and Jim Furyk (68) at two-under after Mickelson missed the cut at the Masters for the first time in 17 years after finishing at five-over.
The three-times champion missed out by a solitary shot after making a mess of the treacherous 12th hole, where he landed in greenside bunkers three times, and signing for a 73.
"I didn't play great. I didn't play bad," Mickelson said. "I just had one bad hole there at 12. And I keep making these triples, they're tough to overcome."
Mickelson was not the only high profile casualty on a day of carnage for former champions. Argentina's Angel Cabrera, the 2009 champion and runner-up last year, missed out after finishing at eight over.
South Africa's Charl Schwartzel, who won in 2011 with birdies on each of the last four holes, also missed out along with 2007 winner Zach Johnson and 2008 champion Trevor Immelman.
With Tiger Woods absent, every Masters champion from 2004 to 2011 will be missing from the weekend while Northern Ireland's Rory McIlroy, who drove into a cabin to blow a four-shot lead on the last day three years ago, was lucky not to join them on the way out of Magnolia Lane.
After an adventurous day in which he made two double bogeys and went searching for his ball in the woods and then azeleas at Amen Corner when his approach hit a sprinkler head, he only survived after draining a tricky six-foot putt on the last hole.
"I've seen a lot of this golf course in the last few years," said McIlroy.
Watson, who won the championship in an epic playoff with Louis Oosthuizen two years ago, followed up his opening 69 with a sparking four-under-par 68, matching the best score of the championship.
The maverick left-hander made his first bogey of the tournament at the ninth hole and also dropped a shot at the last when he missed a short putt but he reeled off five successive birdies from the 12th to seize control of the first major of the year.
"It's not science here," Watson said. "All I'm trying to do is just hit the greens, that means my tee shots are good and two putts, maybe throw in a birdie here or there.
"That's really all I was doing and that's what I've done the last two days and it's worked out so far."
Senden came into the first major of the year in good form after winning last month's Tampa Bay Championship. He was two-over after four holes but stormed up the leaderboard with six birdies in his next 11 holes earning a 68.
With the wind gusting across the course and making the notoriously fast greens even more difficult to read, only a handful of players were able to make up any ground.
Scott made a shaky start, spraying his opening tee shot into a fairway bunker.
He dropped three shots on the front nine before three birdies on the back nine saw him settle for a 72 after his first round 69, the exact same scores he carded when he won the green jacket last year.
"It was very difficult out there today," Scott said.
"Anything even par or better at a major is normally a good score, especially today, I would say. It kept me in the tournament."
Bjorn, playing in the morning when conditions were less tormenting, birdied four of his last five holes while Blixt picked up two late birdies after a double-bogey at the 11th.
"It's a tricky golf course...if you're not quite on, it becomes extremely difficult out here," Bjorn said. "I just tried to do the right things and I executed it well."
Spieth, one of the leaders of golf's new generation, eagled the 15th and then birdied the 18th to show no signs of nerves in his first Masters appearance.
Bill Haas, who led overnight after a first-day 68, tumbled down the leaderboard with a 78, while South Africa's Oosthuizen, who was tied for second after the first day, finished at even-par for two rounds after a triple bogey on the 15th.
The cut was set at 148.
137 Bubba Watson (U.S.)
140 John Senden (Australia)
141 Jonas Blixt (Sweden)
Adam Scott (Australia)
Jordan Spieth (U.S.)
Thomas Bjorn (Denmark)
142 Jim Furyk (U.S)
Fred Couples (U.S.)
Jimmy Walker (U.S.)
143 Jamie Donaldson (Britain)
Kevin Streelman (U.S.)
Kevin Stadler (U.S)
Russell Henley (U.S.)
Stephen Gallacher (Britain)
144 Matt Kuchar (U.S.)
Louis Oosthuizen (South Africa)
Gonzalo Fernandez-Castano (Spain)
Lee Westwood (Britain)
Lucas Glover (U.S.)
Brandt Snedeker (U.S.)
145 Steve Stricker (U.S)
K.J. Choi (South Korea)
Stewart Cink (U.S)
Mike Weir (Canada)
Henrik Stenson (Sweden)
146 Hunter Mahan (U.S)
Vijay Singh (Fiji)
Bernhard Langer (Germany)
Brendon De Jonge (Zimbabwe)
Steven Bowditch (Australia)
Justin Rose (Britain)
Rickie Fowler (U.S.)
Ian Poulter (Britain)
Bill Haas (U.S.)
Larry Mize (U.S.)
Thorbjorn Olesen (Denmark)
147 Miguel Angel Jimenez (Spain)
Gary Woodland (U.S.)
Martin Kaymer (Germany)
Billy Horschel (U.S.)
Francesco Molinari (Italy)
Oliver Goss (Australia)
Thongchai Jaidee (Thailand)
Nick Watney (U.S.)
Chris Kirk (U.S.)
148 Darren Clarke (Britain)
Joost Luiten (Netherlands)
Jason Day (Australia)
Rory McIlroy (Britain)
Jose Maria Olazabal (Spain)
Sandy Lyle (Britain)
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- Thomas Bjorn
- Bubba Watson
- Adam Scott