Jayson Werth and Raul Ibanez also homered for the Phillies, who maintained a three-game lead over the Atlanta Braves in the NL East.
Howard's drive in the third gave him five straight seasons with at least 30 homers and 100 RBIs, setting a new franchise record previously held by Hall of Famer Chuck Klein.
Kyle Kendrick (10-9) gave up hits to his first two batters but settled after that. In six innings he gave up two runs and six hits. He struck out three and walked one.
Kendrick received plenty of offensive support as the Phillies banged out 12 hits. Ibanez had 3 hits, Wilson Valdez went 3 for 4 with a pair of doubles and an RBI, and Shane Victorino also had two hits and increased his hitting streak to 11 games.
The Nationals threatened in the eighth, loading the bases with one out but reliever Ryan Madson got Wilson Ramos to line out to left and then struck out Willie Harris to retire the side.
Brad Lidge pitched a perfect ninth for his 23rd save in 28 chances.
Washington right-hander Jordan Zimmerman (0-2), making his fifth start of the season after undergoing Tommy John surgery last August, allowed six runs on nine hits in three innings. It was the second straight game Zimmerman has lasted just three innings. He has pitched just 20 innings in his five starts.
Washington jumped on Kendrick early. Danny Espinosa opened the game with a single and scored on Ian Desmond's triple. After hitting the next batter, the right-hander settled down, striking out Adam Dunn and Roger Bernadina before getting a groundout for the final out.
Werth evened the score in the second inning by leading off with a homer to left before Valdez put the Phillies ahead for good with a double to left that scored Ibanez.
Philadelphia added three runs in the third, highlighted by Howard's opposite-field shot that scored Chase Utley. Two batters later, Ibanez homered to the opposite field to make it 5-1.
Washington got a run back in the sixth on Michael Morse's two-out single to left that scored Ryan Zimmerman.
Notes: Ryan Zimmerman doubled in the sixth off Kendrick, making him 9-for-17 lifetime against the Phillies right-hander Philadelphia is 27-8 in its last 35 games versus Washington. Philadelphia is 31-11 in its last 42 home games.