Closer La Troy Hawkins (2-1) got the first out in the ninth before Tony Gwynn Jr. reached on second baseman D.J. LeMahieu's throwing error. Ben Revere followed with a single to right. Jimmy Rollins then hit a foul pop that Troy Tulowitzki, a two-time Gold Glove winning shortstop, dropped for an error. But Hawkins retired Rollins on a liner to left. Logan entered and allowed Utley's line-drive single to right that scored Gwynn.
Howard then connected on a 2-2 pitch for his ninth homer.
Jonathan Papelbon (1-1) tossed a perfect ninth for the win.
LeMahieu hit a tiebreaking solo homer in the eighth and Justin Morneau also hit a solo homer for Colorado.
Phillies reliever Mike Adams pitched out of a based-loaded, no-out jam in the seventh after Antonio Bastardo walked the first three hitters. Adams entered and retired pinch-hitter Carlos Gonzalez on a home-to-first double play bouncer to the mound. Adams then struck out pinch-hitter Tulowitzki to end the inning.
But LeMahieu connected off Jake Diekman in the eighth, lining one into the left-field seats. It was LeMahieu's first homer this season in 160 at-bats and fifth in 853 career at-bats.
Phillies manager Ryne Sandberg successfully won a challenge in the fifth inning after second baseman Utley fielded Charlie Culberson's grounder and ran to the bag ahead of Corey Dickerson. Second base umpire Jim Wolf ruled Dickerson safe, but the call was overturned after a video review.
Starters Roberto Hernandez and Jordan Lyles both were effective. Philadelphia's Hernandez allowed two runs and six hits, pitching around five walks in 5 2/3 innings. Lyles gave up two runs and five hits in five innings.
Colorado took a 2-0 lead in the third. Morneau led off with a shot to right for his 10th homer. Dickerson walked and scored on Wilin Rosario's double to left-center.
The Phillies answered in the bottom half. Utley hit his major league-leading 22nd double with two outs. Howard followed with an RBI single to cut it to 2-1.
Marlon Byrd lined an RBI single with two outs in the fifth to tie it at 2. Half of Byrd's RBIs (15 of 30) have come with two outs this season.
Rollins, playing in his 2,000th career game, snapped an 0-for-15 slump with a seventh-inning single. But he was forced at second on Utley's liner to right that Michael Cuddyer caught on a short-hop.
Commissioner Bud Selig, in town to accept an award for his work on cancer education and research, spoke about a variety of topics before the game. Selig said he's pleased with the search committee's process for finding a new commissioner and there's no timetable to pick his successor. Selig also said he's happy with the replay system and he doesn't envision the NL going to a designated hitter unless there's a "catalytic" event. ... Gonzalez wasn't in the starting lineup because of a right calf contusion. He jogged slowly to first on his grounder to the mound. ... The Phillies open a five-game series against the Mets on Thursday night. David Buchanan (1-0) makes his second career start against Zack Wheeler (1-5). ... The Rockies are off Thursday before opening a series at Cleveland on Friday.