Zimmerman reached 200 career home runs with his second shot. Jayson Werth also homered for the Nationals.
Nationals starter Max Scherzer struck out 11, gave up 11 hits and left with a 3-2 lead after the sixth.
Johnathon Papelbon earned his 23rd save in 23 chances, escaping a first-and-third, one-out jam in the ninth. Rafael Martin (1-0) got one out for his first career victory
Johnathan Broxton (1-4) took the loss.
Brandon Moss hit a 454-foot homer for St. Louis, which leads the Pirates by six games with 29 to play in the NL Central.
