Maholm (10-7) retired 14 straight batters and allowed just one runner as far as third base. Sixty-four of his 95 pitches were strikes.
The left-hander, obtained in a trade last month from the Chicago Cubs, notched his first victory as a Brave after dropping his Sunday debut. He didn't issue a walk and fanned five.
Jason Heyward and Dan Uggla each socked a two-run homer for Atlanta, which took the opener of a three-game set and its sixth in eight games overall.
Matt Harvey (1-3) was tagged with the loss after giving up two runs on just two hits over six full innings for the Mets, who fell to Atlanta for the sixth straight time.