The Phillies won their second straight and remained six games in front of Florida for the lead in the National League East.
Washington overcame a 4-1 deficit to tie it in the seventh, but reliever Tyler Clippard (2-2) served up homers to the first two men in the eighth in the span of four pitches.
Werth also had an RBI single and Raul Ibanez doubled twice.
Starter Cliff Lee (6-2) got the win while giving up five runs on 10 hits over seven-plus innings.
Washington has lost 10 of its last 11 games. Philadelphia has captured its last nine meetings with the Nationals.
Copyright 2009 by United Press International.