Halladay (14-4), pitching in his hometown, allowed five runs on eight hits in seven innings. He struck out seven and walked one as the NL East-leading Phillies won their sixth straight.
Brad Lidge got three outs for his first save of the season after being reinstated from the disabled list late last month. Four of his five appearances, including his latest outing, have been scoreless since his return July 25 from a right rotator cuff strain.
It was the third homer in two games for Howard, whose two-run double capped a four-run outburst in the second. The Phillies were hanging on to a 6-5 lead in the sixth when Howard followed Chase Utley's two-out single with a drive into the center field bleachers off reliever Rex Brothers for his 24th home run of the season.
Howard hit two solo homers in Philadelphia's 5-0 victory over the Rockies the night before. The Phillies' only previous sweep in a series of three or more games at Colorado came May 7-9, 1999 (also 3-0).
The Rockies were swept in a home series for the first time this season.
Jason Hammel (6-11) gave up six runs on eight hits in five innings in taking the loss, which was the Rockies' fourth straight.
Hammel walked the first three batters he faced but limited the damage by fanning Howard and Raul Ibanez around Hunter Pence's sacrifice fly.
Colorado went ahead 2-1 in its half of the first, helped by an unearned run that came around on first baseman Howard's double error. Howard first bobbled Dexter Fowler's grounder, allowing him to reach, and then botched the throw to Halladay, covering first, to allow Eric Young Jr. to score from third. Fowler later scored on Troy Tulowitzki's sacrifice fly.
Hammel's control problems resurfaced in the Phillies' four-run second and again in the fourth, when Philadelphia took a 6-4 lead.
Jimmy Rollins hit successive RBI singles, and after Utley was hit by a pitch, Howard hit a two-run double over center fielder Fowler's head.
The Phillies loaded the bases with two outs in the fourth and Halladay - who singled, took second on a grounder and went to third after a walk - came home on a wild pitch by Hammel in the dirt that skipped past catcher Eliezer Alfonzo.
The Rockies kept it close with RBI singles in the second and third by Alfonzo and Helton, who added a run-scoring groundout in the fifth. Helton drove in his third run of the day with a solo homer in the eighth off reliever Antonio Bastardo.
NOTES: The Phillies are 19-4 in Halladay's 23 starts this season. ... Philadelphia, in the midst of a 20-game stretch without a day off, has gone 10-3 so far. ... Rockies OF Carlos Gonzalez, on the 15-day disabled list with strained right wrist ligaments, was scheduled to begin a three-game rehab assignment with the team's Triple-A affiliate in Colorado Springs. He's expected to rejoin the Rockies on Saturday and, barring a setback, could be reinstated from the DL. ... The Phillies head to San Francisco to open a three-game series against the defending World Series champions. LHP Cliff Lee (10-7) is slated to start Thursday night's opener and will be looking to build on an impressive career record against the Giants. He's 3-0 with a 1.13 ERA but last started against the Giants in the regular season on July 31, 2009, when he threw a four-hitter at San Francisco. ... Young has stolen a base in four of his last five games. ... Mark Ellis' third-inning single snapped an 0-25 skid.