Using a weird-looking putting grip he calls the saw, O'Meara took the Desert Classic by one from Paul McGinley to end a slump which had seen him fall from fourth in the world to 201st.
The former Masters and Open champion was handed the €267,750 first prize after a closing 69 gave him a 17-under-par total of 271.
He then celebrated his return to form in the company of close friend Tiger Woods, who had offered him a lift back to the US on his private jet and with whom he had visited US troops on the aircraft carrier George Washington on Wednesday.
Woods threatened to force his way in the hunt when he turned in 32 and then eagled the long 10th, but bogeys at the 14th and 17th killed off his challenge and he ended joint fifth.
Irish Ryder Cup hero McGinley was seeking his first win since he holed the putt that sank the United States at The Belfry two years ago. The shot that cost him his chance came on the 425-yard 16th.
His drive finished behind a tree and the resulting bogey put him two behind. He did have an eagle putt on the par-five last, but it was from over 60 feet and although the pace was good the line was slightly off and he had to be content with a birdie.
O'Meara had laid up short of the water, played an excellent pitch and two-putted for the title. After managing only one top finish all last season and ending it a worst-ever 143rd on the American tour it was easy to understand his delight.
"This is a big day for me," he said. "It's been a long time and it gives me a huge boost in confidence. At 47 maybe it tells me I can still do it. Chalk one up for the old boys," he said.
McGinley had himself dropped from fourth in the world to 159th, but now he will look to build on this and keep his Ryder Cup spot in September.
Briton David Howell, looking for a cup debut, shared third place with world number three Ernie Els, who like Woods closed to three behind, but ran out of holes.
McGinley, who O'Meara thinks could have a big year, said: "It was a really good week, but I'm disappointed not to have won.
"We're in a competitive business and the difference between first and second is huge. I feel like I've been in a boxing match. It was mentally tough and to be as tough as Mark was you have to hand it to him," said McGinley.
"I don't feel I lost it. Considering he had not won since 1998 he played awesome he never seemed to give me an inch.
"He played like a guy who had been winning tournaments every day of his life and I can see why he has been so successful."
Woods made no secret of the fact he was rooting for his buddy.
"We all want to see him do it," he said. "He's 47 and Paul has many more years," he said.
"It's all been about his putting. He's been playing decent, but not making anything. He tried 'the claw' (another unusual grip) and a belly putter, but he just needed to feel that he could release the blade consistently."
Woods has no intention of adopting the same method, though. "I've tried lots of different ways for fun, but my stroke gets worse. I'm doing all right the way I do it.
Els admitted he was frustrated not only by some putting lapses, but also some "silly mistakes."
He had seven birdies in his first 14 holes, but needed a repeat of his course-record 62 to put the heat on and parred in for a 65. It was still the best round of the day. Colin Montgomerie dropped to 12th.