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.
Swim Week Miami Beach 2014 [PHOTOS]