The 36-year-old appeared to poke the ball over the line but the referee did not award the goal, until a video review overturned the decision.
However, the Galaxy were unable to hold on to the lead as their winless run extended to five games following Carlos Vela's equalizer from the spot six minutes into the second half.
The result left the Galaxy fifth in the Western Conference and five points adrift of second-placed LAFC.
Martinez, meanwhile, broke the league's regular-season scoring record with his 28th goal of the campaign.
Martinez surpassed the achievements of Bradley Wright-Phillips (2014), Chris Wondolowski (2012) and Roy Lassiter (1996) with his 74th-minute strike in Orlando.
Orlando's Scott Sutter had cancelled out Leandro Gonzalez Pirez's opener before half-time.
The win sent Eastern Conference and Supporters' Shield leaders Atlanta five points clear atop the standings amid their seven-match unbeaten streak with eight regular-season games remaining.