The hard-serving Isner avenged his only loss to Ebden in five career ATP Tour meetings when the Aussie beat him earlier this year at the Australian Open.
"It was tough," Isner said. "Just like yesterday, I was able to get out early in the third set and that definitely took some pressure off.
"I'm very happy to be back in the final here."
In the final the 33-year-old Isner will face fellow American Ryan Harrison, who beat Britain's Cameron Norrie 2-6, 6-3, 6-2.
Isner has won eight of his nine semi-finals in Atlanta, and will look to improve his record of 13-12 in finals.
Isner appeared to be cruising to victory, leading by a set and up by a break, when the wheels almost fell off.
The fourth-seeded Ebden broke back in the second and then saved one match point in the ensuing tie-break when Isner flubbed a backhand return.
Isner rebounded by breaking Ebden twice in the deciding set. He smashed 26 aces, using the confidence from his victory at the Miami Open and run to the Wimbledon semi-finals to win in exactly two hours.
That helped set up the second straight Isner-Harrison Atlanta final with Isner triumphing last year.
"I know a lot about Ryan," Isner said. "There are no secrets there. We are good friends and it’ll be a rematch of last year, so it’ll be cool."