Pujols has nine home runs for the season and his solo shot in the opening inning was one of three round trippers given up by losing pitcher Jordan Zimmerman (2-1).
Washington's two runs came on a homer by Willie Harris in the seventh.
Todd Wellemeyer (2-2) got the victory, giving up six hits and two runs over seven frames.
Ryan Zimmerman went 2-for-4, extending his hitting streak to a Nationals' record 20 games.
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