'It was ... all guess and a lot of fun when it went in,' Couples said of the birdie putt worth $220,000.
In this event's skins format, players must win or tie the hole following their win to validate.
Couples, 44, the event's first two-time winner, made the most money, netting $270,000, including $50,000 for being closest to the pin five times on the par-3 course.
Lee Trevino won a three-hole playoff with a birdie to claim the final $80,000 in the skins at Treetops Resort. Trevino and Masters champion Phil Mickelson tied for second, winning $130,000 apiece.
Mickelson won a $60,000 skin on hole No. 14 with a 10-foot putt and validated at 15 with a par. He also was closest to the pin seven times, four on Tuesday.
Trevino had his one final skin and was closest five times in the two rounds. Fuzzy Zoeller won $10,000 for being closest to the pin once Monday.
Three times validation attempts failed on Monday, which sent all nine holes of skins money to the second day. Each hole was worth $20,000.
Another long putt forced extra holes in the competition.
Trevino made a 54-foot putt on the final hole of regulation for birdie, keeping Mickelson from winning the final $80,000, a skin that didn't require validation.
Trevino won the sudden-death playoff on the 21st hole with an 8-foot putt.
'Believe it or not, I was just trying to get it close, and it went in,' Trevino said of the putt that forced the playoff. 'Anything over 15 feet, well you need a little luck, and I was lucky there.'
Couples, who won $440,000 in his 2002 Par-3 Challenge win here, said his validation putt made him nervous.
'In my career I've missed so many, and made a few,' he said. 'It's nice when they go in and you win.'
Fred Couples -- $270,000
Phil Mickelson -- $130,000
Lee Trevino -- $130,000
Fuzzy Zoeller -- $ 10,000
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