Pittsburgh scored a total of just three runs while getting swept and headed home, looking to get back to their winning ways and erase the memory of their trip to Washington.
''We had a tough series,'' said Pirates manager Clint Hurdle, whose team is off on Monday. ''We get to go home and unpack our bags. We love to play at home and we love our fan base. We look forward to that.''
Morton (5-1) had won all five of his starts this season, and came into the game with a scoreless streak of 14 1-3 innings. But the Nationals erupted for the biggest first inning in their history as Bryce Harper and Yunel Escobar homered, and Morton was charged with all nine runs while getting just two outs.
''My stuff was fine,'' he said. ''The good pitches I made, they hit them. The bad pitches I made, they hit them, and that's embarrassing. Nothing I was doing was working.''
Gonzalez (5-4) pitched seven shutout innings, the latest top effort from a Washington starter.
Harper hit his 24th homer, extending his career high and connecting in his second straight game after sitting out Friday with a tender hamstring.
Gonzalez gave up four hits, struck out four and walked two. This came after he allowed five runs and eight hits in just 3 1-3 innings at Tampa Bay in his previous start.
Gonzalez passed the injured Stephen Strasburg for second on the Nationals' career victory list with 47. He also hit an RBI double.
After Morton retired the first batter, Escobar singled and Harper homered. The Nationals batted around, and Escobar's three-run homer finished Morton and brought Vance Worley from the bullpen.
Pirates: Open a three-game series with visiting Cincinnati on Tuesday.
Nationals: Start a three-game series with visiting Atlanta on Tuesday.
Pittsburgh's Jose Tabata was booed during each of his at-bats. He ended Scherzer's bid for a perfect game with two outs in the ninth inning when he was hit by a pitch - many thought he lowered his left elbow a bit to get nicked.