Lee (9-2) racked up his ninth straight start without a loss, holding the Nationals to two runs on five hits. The ace left-hander didn't issue a walk in throwing 82-of-110 pitches for strikes.
Jonathan Papelbon hurled a scoreless ninth for his 14th save as the Phillies clinched their three-game set against Washington.
Nats starter Ross Detwiler (2-5) absorbed the loss, yielding four runs on seven hits over six full frames.
Jeff Kobernus socked his first major league homer and Jayson Werth also went deep for Washington.