Bowditch, who got married at the resort next to the TPC Four Seasons five years after attempting suicide at his Dallas home while battling depression in 2006, had 27 birdies while becoming the seventh player to lead all four rounds of the event. He finished at 18-under 259 on the rain-altered layout.
Charley Hoffman (65), Texan Jimmy Walker (66) and Scott Pinckney (66) tied for second at14 under. Zach Johnson shot 63 to finish alone in fifth at 13 under.
Hometown favorite and Masters champion Jordan Spieth finished 7 under after an even-par 69.
Playing with Bowditch in the final group, Dustin Johnson briefly overtook him early in the round before making an 8 at the par-4 sixth. He finished at 11 under with a 69.
A sunny day wrapped up two otherwise soggy weeks of golf in Dallas-Fort Worth, including a 5-inch overnight downpour after the first round of the Nelson that turned one of its toughest holes -- the par-4 14th -- into a pitch-and-putt par 3 of barely 100 yards for the final three rounds.
While birdies were the norm after easy wedge shots from what might normally be a drop area in front of a greenside pond, Bowditch had to save par from about 12 feet to keep a three-shot lead, pumping his right fist after the ball dropped in.
The temporary tee box was about 20 yards farther back Sunday, and tour officials believe par of under 70 was a first according to records going back to 1983. The overall par total was 277.
Up by three at the spectator-friendly 17th, Bowditch leaned like he thought his tee shot on the par 3 might go in the water to the right of the green. Instead, the ball landed safety on the back of the green, and Bowditch -- who won the 2014 Texas Open in San Antonio -- raised his putter as the ball birdie putt rolled in the punctuate the win.
Spieth had an opening birdie but quickly gave it back at the par-3 2nd. He went in the water twice for bogeys on the back nine, including on 17 a day after he gave big galleries that followed him all week their biggest thrill by almost hitting the pin on the fly on the 198-yard hole.
After getting within three shots of the lead halfway through the tournament, Spieth never did threaten and ended his streak of second-place finishes in all three previous Texas events this year. The 21-year-old Dallas player tied for 30th five years after finishing 16th in his first tour event as a 16-year-old amateur.
Johnson birdied two of the first three holes even though he missed the first four greens, but the erratic start caught up with him at No. 6. Johnson went out of bounds to the right off the tee, then way left into tall grass off the rough with his second tee shot. It took him three swings to get out on his way to a quadruple bogey.
Walker also held the lead on the front nine but missed short putts for par on 11 and 12. He tried to make a late run with an eagle chip at the par-5 16th and a birdie on 17, but Bowditch answered with birdies on both holes.