Shane Victorino had two hits and scored twice. The All-Star center fielder had no problems with the crowd, a day after he was doused with beer while catching a fly ball, prompting Victorino to file a police report.
Police said the incident was being investigating as a "simple battery." Victorino got a personal apology from Cubs chairman Crane Kenney before the game, and it was not immediately known if there was increased security in the bleachers.
The Phillies posted their first sweep at Wrigley Field since June 14-17, 1984, when they won four straight.
Lee (3-0) allowed one run and six hits over eight innings. He struck out eight and walked three to win his sixth straight start overall. He also helped himself with a double.
The reigning AL Cy Young winner also got victories in his last three starts with the Cleveland Indians before being traded to the World Series champions on July 29.
Howard hit his 27th homer, a three-run shot off Ryan Dempster (6-6). Two batters later, Feliz added his ninth of the season, a solo drive for a 4-0 lead.
Feliz hit an RBI single in the fifth to make it 5-1, and Chase Utley delivered a run-scoring single in the seventh.
Chicago got its run in the fifth on Jeff Baker's double, a sacrifice and RBI single by Ryan Theriot.
The Cubs threatened in the second when two walks and Jake Fox's single loaded the bases, but Lee fanned Dempster to end it. Dempster, in his fourth start since coming off the disabled list with a broken toe - an injury he got hopping over the dugout railing - gave up a leadoff single to Victorino in the fourth. After Utley worked a walk, Howard sent a high fly to left field that carried into the seats and put the Phillies ahead 3-0. Feliz's homer also sailed into the left-field bleachers.
NOTES: Lee pitched against the Cubs at Wrigley Field in June while still with the Indians. Cleveland led 7-0 in that interleague game, and Lee departed after seven innings with the Indians ahead 7-2. Chicago rallied for an 8-7 victory in 10 innings. ... Theriot reached a career-high 46 RBIs with his fifth inning single. He drove in 45 in 2007.