Brad Guzan had three saves for his MLS-leading 10th shutout this season.
Atlanta (11-8-3) controlled the action throughout - finishing with 71.4% possession and outshooting D.C. United 18-7 - and finally broke through as time waned. Darlington Nagbe lofted a cross that Martínez headed home from point-blank range to open the scoring in the 89th minute. Josef Martínez slipped behind the defense, ran onto a long ball from Gonzalo Martínez flipped it over the head of charging goalkeeper Bill Hamid and into the net in the second minute of stoppage time.
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D.C. (9-6-8), which has just one win its last five games, fell into third in the Eastern Conference standings, one point behind Atlanta (36) and four back of Philadelphia.
Josef Martínez chipped a penalty kick over the crossbar in the 72nd minute. It was just the second times in 17 tries in MLS that he failed to convert from the spot.
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