He yelled "Fore left!" a second after impact on the 202-yard hole.
"It was just very bad timing," Mickelson said about the tee shot. "Quick from the top, lower body fast. Just a bad swing. I did the same thing on the next par 3 with the same club. Only it went the other way. I made par both times, though."
Recovering from flu-like symptoms, the 42-year-old Mickelson had three birdies, a bogey and a double bogey at La Quinta Country Club one of three courses used in the pro-am event that he won in 2002 and 2004 to drop nine strokes behind the first-round leaders.
"I felt a lot better," Mickelson said. "I took it easy on Monday and Tuesday. It was like Day 10, but I'm fine now. I'm 95 percent better."
Jason Kokrak, Roberto Castro and James Hahn topped the leaderboard at 9-under 63.
Kokrak had two eagles and five birdies at La Quinta.
"I just tried to put it in the right spots, put it in the fairways," Kokrak said. "Out there, that's key. They're tighter fairways and if you can be in the fairway, you'll have a good opportunity for birdie."
Castro had nine birdies at PGA West's Jack Nicklaus Private Course, and Hahn had nine birdies on PGA West's Arnold Palmer Private Course.
"It was a great day," Hahn said. "Chipped two in. Hadn't done that since I was nine."
Russell Henley, the Sony Open winner Sunday in Hawaii in his first start as a PGA Tour member, had a 64 on the Nicklaus course. He's 32 under in his first five rounds this year.
"It was a perfect day," Henley said. "The weather is perfect. The greens were true. So, it's just trying to stay patient and let the birdies come to me."
Mickelson made his first start since tying for second in early November in the HSBC Champions in China, the only event he played after the Ryder Cup.
"My timing and rhythm was off a little bit," Mickelson said. "My putter was atrocious and I've been putting great, too. So, that was disappointing."
Mickelson made his second brilliant recovery shot on the par-5 13th, slicing a fairway wood from the rough on the adjacent 14th hole high over trees and onto the green. However, his eagle try ran 12 feet past the cup and he three-putted for par.
"Gosh, I hit such a great 5-wood to 35 feet for eagle," Mickelson said. "To three-putt that is just, it was just a lot of rough stuff today."
He also scrambled to save par on the par-3 15th, this time shouting "Fore right!" after another poorly timed swing. Turning to the flop shot again, he lobbed the ball over the corner of a bunker to 4 feet.
"When I'm not playing for a while, I really get excited to get back out and I was really amped up," Mickelson said. "I was nervous today and excited to play and maybe a little over-amped because again everything was quick my rhythm, timing, everything."
Mickelson bogeyed the par-3 third, three-putting from the back fringe, and birdied the par-5 fifth after driving left into a fairway bunker and being forced to lay up. He made a double bogey on the par-4 10th after an aggressive drive over the trees went out of bounds.
"That hole has my number," Mickelson said. "This time, it hit a tree, hit the cart path, went out of bounds by a foot. So, that hole is just my nemesis."
He got one of the strokes back with a two-putt birdie on the par-5 11th, and got back to even par with a birdie on the par-4 18th, hitting an 8-iron from 168 yards to 3 feet.
"I hit a lot of fairways and was able to shake out an even-par round," Mickelson said. "As bad as that is, I've got a low round in me tomorrow, I think. It doesn't feel like it's far off."
Aaron Baddeley, Greg Chalmers and Doug LaBelle II matched Henley at 64. Baddeley played the Palmer course, and Chalmers and LaBelle opened on the Nicklaus course.
Mike Weir, the 2003 champion, opened with a 67 at La Quinta. The Canadian left-hander has missed 16 consecutive cuts and has finished only one tournament a tie for 70th in the AT&T National in July 2011 in his last 28 events.
"I drove it well and putted well and everything was pretty good," Weir said. "It was a nice solid round to get off to a good start."
FedEx Cup champion Brandt Snedeker also had a 67 at La Quinta. He's the highest-ranked player in the field at No. 8 in the world.