Atlanta star Martinez scored in his 13th successive league match but Frank de Boer's side still lost to Philadelphia in Sunday's (AEST) top-of-the-table clash.
Martinez broke the deadlock in the second minute of first-half additional time , the Atlanta forward combining with Darlington Nagbe before finding the back of the net in front of a sellout crowd at Talen Energy Stadium.
However, Union scored three unanswered goals in the second half to beat Atlanta, which claimed the US Open trophy during the week.
Brenden Aaronson equalised in the 61st minute before Union pair Kacper Przybylko and Sergio Santos scored during the final four minutes in Philadelphia.
Union clinched a play-off spot in the process as it moved top of the east on 51 points, a point clear of New York City and three ahead of Atlanta.
New York City FC booked a post-season berth thanks to a 3-1 win at lowly Vancouver Whitecaps.
DC United is fourth in the Eastern Conference thanks to their 3-0 victory over Montreal Impact in the absence of suspended captain Wayne Rooney, with New York Red Bulls slipping to fifth after a 2-0 loss to Colorado Rapids.
Elsewhere, Chris Wondolowski scored twice as San Jose Earthquakes accounted for Orlando City 3-0, Real Salt Lake went down 1-0 against Portland Timbers, Sporting Kansas City edged Houston Dynamo 1-0, FC Dallas defeated FC Cincinnati 3-1, New England Revolution and Toronto FC played out a 1-1 draw, while Columbus Crew drew 1-1 with Chicago Fire.