Hunter Pence doubled twice and Shane Victorino and Raul Ibanez each singled and scored a run for the Phillies, who have won five straight.
Kendrick (6-5) yielded four hits, struck out a career-high seven and walked two in his longest outing in 11 starts this season. He threw a career-high 117 pitches and didn't allow a runner past second base.
The Phillies got off to a fast start against Aaron Cook, who pitched four innings before leaving with muscle spasms in his neck.
Jimmy Rollins led off the game with a walk and moved to third on Victorino's single. Chase Utley drove in Rollins with a bouncer to shortstop and Victorino scored on Pence's two-out double.
Philadelphia tacked on two more in the fourth. Howard led off with a drive to the facing of the second deck in right-center. One out later, Ibanez and Placido Polanco hit consecutive singles and Ibanez scored on Brian Schneider's sacrifice fly to center.
Cook (2-6) gave up five hits, struck out two and walked one. Howard led off the eighth with a drive to left off Matt Lindstrom for his 23rd homer.
David Herndon pitched a 1-2-3 ninth to finish the shutout. The Rockies had very few chances against Kendrick and failed to capitalize on any of them. They had two men on in the first but Seth Smith looked at strike three to end the threat. Eric Young Jr. and Chris Iannetta reached second base in the third and fifth, respectively, but were stranded there.
NOTES: Howard has two multihomer games this season and 27 for his career. His last multihomer game was April 29 against the Mets ... Phillies ace Roy Halladay will start Wednesday's series finale against Jason Hammel. Halladay, who is from Arvada, Colo., made his first start at Coors Field on May 12, 2010, and got a no-decision. He is 2-0 with a 0.77 ERA in three career starts against the Rockies. Hammel is 1-1 with a 5.40 ERA in three career appearances against Philadelphia, two of them starts.