The visitors made the breakthrough when Joe Garner headed in a long ball in the 15th minute.
Fondop doubled Latics' lead in the 58th minute and then grabbed his second 30 minutes later, effectively killing the game off for the hosts.
Sam Beckwith delivered a late consolation for Maidenhead.
Delighted Latics boss Micky Mellon said: "We played very well.
"I think over the course of 90-odd minutes we absolutely deserved the result and played some really good football."
Latics are back in action on Tuesday night when they travel to York City.
