Frenchman Roger-Vasselin saw off top seed Isner 6-4 4-6 6-4, while qualifier and former champion Ernests Gulbis beat number two Tommy Haas 6-3 4-6 7-6 (7/2).
Roger-Vasselin had already overcome one formidable serve at Delray Beach in the shape of Ivo Karlovic and was straight back into the groove as a single break gave him the first set against Isner.
Isner battled to take the second, but Roger-Vasselin broke in the first game of the third, then held his serve in a game which both players had chances to win and Isner could not find a way back.
Isner will take on Gulbis after the Latvian came out on top in a battle of two former Delray Beach champions.
The final pits the world number 105, Roger-Vasselin, against the man ranked four places beneath him.
They have never faced each other before at ATP Tour level.