Aaron Baddeley finished two strokes off the pace at 3-under-par 285. The young Australian was followed by Barry Cheesman at 1-under-par 287.
'This is a life-changing experience for me,' said Thatcher, who became the sixth rookie to win on tour this season. 'This is a dream come true for me. I honestly won't know the full extent of this for a while.'
Thatcher carried a five-stroke lead into the final round and the advantage held up despite a rocky day at the difficult Bayonet Course. After a bogey at the opening hole, Thatcher seemed to regain control with back-to-back birdies from the third. However, he bogeyed the fifth and three-putted for bogey at the par-4 ninth to make the turn at minus-6.
'I was OK until I missed that putt on nine,' said Thatcher. 'From there on it was just a mental grind. I had to try and not get ahead of myself.'
The 25-year-old did what he could with a birdie at the 10th, but faltered with bogeys at the 12th and 14th. Thatcher countered with a birdie at the 15th after his approach landed within inches of the cup, but ran into trouble again with a bogey at the very next hole.
Thatcher then buckled down and parred the two remaining holes for his maiden win.
'I've never been so shaken so bad my entire life over short putts and shots from the fairway,' said Thatcher, who collected $81,000 for the win. 'I'm glad I started off with such a big lead because I tried to give it away a couple times. Aaron was only a couple of putts from pulling it off.'
Baddeley got off to a good start with a birdie at the par-5 first, but could not make a move the rest of the way. He dropped a shot at the 12th and picked up a birdie at the 14th for a round of 71.
'I played great today,' said Baddeley, who posted his third top-10 finish of 2002. 'I hit it well and putted well. I kept trying to put pressure on him by hitting good shots.'
Charles Warren, who won the Charity Pro-Am at the Cliffs in April, shot a final-round 73 to finish alone in fourth place at even-par 288.
Vic Wilk and Anthony Painter were six shots off the lead at 1-over-par 289.
Todd Barranger and Mark Wurtz finished tied for seventh at 2-over-par 290. They were followed by Jason Caron, Erik Meeks and Omar Uresti at 3-over-par 291.
Final results from the Bank of America Monterey Peninsula Classic