The American Henry held off a late charge by Brazilian Alexandre Rocha for a one-point triumph in a tournament being played under Modified Stableford scoring in Nevada.
Under the scoring system, at the only tournament which uses the method, an eagle brings five points while a birdie brings two, a bogey minus one and a double bogey or worse is minus three points.
Henry took a three-point edge into the final round and fended off the competition with four birdies and one late bogey that gave him his first win since the 2006 Buick Championship, now known as the Travelers Championship.
It's been a long time coming," Henry, a former Ryder Cup player, said.
"Rocha played great down the stretch to make it interesting. This means a lot."
Henry, who led the Byron Nelson Championship in May with two holes to play but let it slip away, briefly lost the lead on the par-4 fourth Sunday but he responded with three birdies in his next four holes to separate himself.
His close approach shot to the 15th for birdie left him six points clear, and allowed him to survive a bogey as well as back-to-back birdies from Rocha on the final two holes.
Rocha finished the round with five birdies and one bogey.
Argentine Andres Romero finished six points behind for solo third while mercurial American John Daly ended up tied for fifth with Justin Leonard.
Three-time major champion Padraig Harrington of Ireland stumbled home with two bogeys and a double-bogey in his final round and had to settle for a tie for 19th.