Isner will meet fellow American Ryan Harrison in Sunday's final after the eighth seed prevailed over Britain's Cameron Norrie 2-6 6-3 6-2 in less oppressive evening conditions.
Isner served 26 aces against Ebden, who appeared to be hindered by a sore neck and served 15 double-faults.
"I benefited from my opponent not being 100 percent," Isner said.
"Of course I’m very happy to be back I the final here."
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Isner won his fourth Atlanta title when he beat Harrison in last year's final.
"I know a lot about Ryan," Isner said. "There are no secrets there."
(Reporting by Andrew Both in Cary, North Carolina; Editing by Peter Rutherford)
