Werth's leadoff drive on a 3-1 pitch from Tyler Clippard (2-2) gave the Phillies a 5-4 lead. It was his second in two games and No. 33 on the year.
Feliz followed with his 10th of the season, a shot that landed in the left-field seats beyond Philadelphia's bullpen.
It was the Phillies' 10th set of back-to-back homers and second in two games. Werth and Raul Ibanez had consecutive drives in the seventh inning of Philadelphia's 5-3 win over the Nationals on Tuesday night.
The Nationals loaded the bases with no outs in the eighth and only came away with one run. Chan Ho Park replaced Lee with runners on first and second and walked Elijah Dukes before retiring three straight pinch hitters. Willie Harris flied out, Pete Orr had a sacrifice fly and Wil Nieves grounded out.
Phillies manager Charlie Manuel then opted for Madson in the ninth. Justin Maxwell led off with a single and stole second before Cristian Guzman struck out. Adam Dunn then lined into a game-ending double play.
Lidge picked up his 10th blown save Saturday and was pulled in the ninth inning of Philadelphia's win Tuesday. Manuel hinted before Wednesday's game that Lidge may lose his closer role.
"These are very important games, and we need to win, and I'm going to pitch on that night who I think can do the job," he said.
The Nationals tied it at 4 in the seventh. Alberto Gonzalez led off with his third double of the game and advanced on pinch-hitter Jorge Padilla's bunt single. With one out, Guzman hit a grounder to shortstop Jimmy Rollins that looked like a double play. But second baseman Chase Utley lost the ball as he tried to transfer it to his throwing hand, allowing Gonzalez to score.
Philadelphia scored three times in the second to take a 3-1 lead. Werth hit a run-scoring single, Lee picked up his first career RBI with a bases-loaded single and Jimmy Rollins drove in a run with a groundout.
Dunn had RBI singles in the first and fifth, and Guzman also singled in a run for the Nationals.
NOTES: Phillies LHP Scott Eyre was sent to Philadelphia to have his sore left elbow examined. ... Phillies LHP Jamie Moyer will start Saturday against New York in place of J.A. Happ, who was scratched from Monday's start with an oblique strain. ... Philadelphia promoted LHP Sergio Escalona and 1B Andy Tracy from the minors. ... Nationals C Jesus Flores pinch hit in the fifth, his first appearance after missing 106 games with a right shoulder injury. Flores grounded out. ... Gonzalez's three doubles were a career high.