Neither team was able to dent the scoreboard until the Brewers mounted a charge in the eighth against Drew Storen (2-2).
Logan Schafer collected a lead-off single and stole second to start the frame, and Rickie Weeks then drew a walk. One out later Francisco smashed a pitch that one-hopped the wall in right-center field, scoring both runners for the game's first runs.
Martin Maldonado and Jeff Bianchi each added an RBI later in the frame as the Brewers avenged a 10-5 loss in the Monday opener of the four-game set.
Jim Henderson (3-2) got the win after starter Wily Peralta had tossed 5 1/3 shutout innings.
Nationals starter Stephen Strasburg was saddled with a hard-luck no-decision despite hurling seven scoreless innings, during which he allowed just three hits and struck out eight to go along with four walks.