Zimmerman (1-1), plagued by a lack of run support in his first three starts while compiling an ERA of 1.29, allowed only a solo homer to Orlando Hudson in the fifth. He helped his own cause with an RBI single during a two-run second that put the Nationals in front for good.
Washington improved the best record in the National League to 14-4 while the Padres have the worst mark in the league at 5-14.
The Nationals were protecting a 2-1 advantage before breaking loose for a four-run seventh. Adam LaRoche singled in a run in the inning, Jayson Werth drew a bases-loaded walk and Wilson Ramos had a two-run base hit.
Tom Gorzelanny worked the final three innings, which qualified him for his first save of the year.
The loss went to Joe Wieland (0-3), who allowed two runs on five hits and struck out four over six innings.
Washington has won the first two outings in a six-game road trip. After concluding its series against the Padres on Thursday, Washington moves on to Los Angeles.
Ray Liotta sues skin care company over use of likeness
Boston schools pull out free condoms over wrapping complaints