Watson beat Justin Thomas 3&2, a result that prevented second seed Thomas from assuming the world number one ranking.
American 32nd seed Kisner outlasted Swedish 13th seed Alex Noren 1-up at the first extra hole in the other semi-final in benign conditions at Austin Country Club.
Noren had a seven-foot birdie putt to win at the 18th hole but he missed it after allowing for too much break.
It was a mistake he lived to regret because Noren subsequently made a complete mess of his long approach putt from off the green at the 19th hole, the par-five 12th, and could not make birdie.
That gave Kisner a chance to win the match with a five-foot birdie, and he sank it dead centre.
"It was a tough match," Kisner told Golf Channel.
"He kept hitting it in there close. If he had made any of those putts it would have been tough to come back from, but I hung in there and made putts when I needed."
"I'll see if I can drive it within 100 yards of him," Kisner said of the prospect of playing the long-hitting Watson in the 18-hole final.
Watson had time for a leisurely lunch while the other semi-final ran long.
"I made one mistake (choosing the wrong club at the par-three seventh. Apart from that) I didn't really make any mistakes," two-times Masters winner Watson said.
"I made some putts early. I just played solid and he didn't make any putts."
After playing brilliantly for most of the week, Thomas was slightly off his game, hitting a series of shots that were surprisingly poor by his own high standards.
Watson is seeded 35th despite his recent return to form highlighted by a victory at the Los Angeles tour stop at Riviera in February.
His relatively low ranking is due primarily to last year's mediocre form that caused him to plummet down the list. (Reporting by Andrew Both in Cary, North Carolina; Editing by Clare Fallon)