Zimmerman went 2 for 4 with two RBI. His run-scoring single in the fifth gave the Nationals the lead for good at 2-1.
Werth, who went 2 for 4, added a solo homer off San Diego starter Andrew Cashner (5-13) in the sixth. Zimmerman greeted reliever Kevin Quakenbush with a homer to start the seventh.
Zimmerman finished the series with eight RBI in three games.
Ross (5-5) won his second straight start, allowing the bunt single by Corey Spangenberg and one run in six innings. The right-hander struck out seven and walked two.