Isner finished with 13 aces, but Davydenko saved three break points and broke the big-serving American once in the first set.
Davydenko, once ranked No. 3, next plays the winner of the match between Brian Baker of the U.S. and Mikhail Kukushkin of Kazakhstan.
Simon, who grew up in Nice, did not face a single break point in a 7-5, 6-0 victory over Brazil's Thomaz Bellucci. He will face Almagro for a place in Saturday's final. The Spaniard beat Belgium's Steve Darcis 6-4, 6-4.