Michael Barrett contributed to the victory with two RBI as the Padres improved to 4-4 on their 10-game homestand.
Starter Randy Wolf limited the Nationals to two runs on seven hits with five strikeouts in six innings, but it was reliever Heath Bell (1-3) who got the win. Bell and Bryan Corey combined for two scoreless innings in the seventh and eighth. Trevor Hoffman was perfect in the ninth for his 10th save.
Aaron Boone hit a two-run homer for Washington, which has lost five of seven.
Nats reliever Charlie Manning (0-1) took the loss for giving up the home run to Gonzalez. Joel Hanrahan gave up the next homer to Kouzmanoff. Washington starter Shawn Hill allowed two runs on five hits and five runs over five innings. He also struck out five.