The Mets, who had dropped three straight, broke a 13-game stretch in which they scored three runs or less against the NL East-leading Braves.
Tim Hudson (15-6) lost for the first time in nine starts after allowing eight hits and four runs - three earned - with one walk and four strikeouts in seven innings.
Santana (11-9) left after five innings, his shortest outing in 23 starts, throwing 65 pitches. The Mets announced that the left-hander had a strained pectoral muscle and was listed as day-to-day.
Santana allowed three hits, one run and one walk with three strikeouts to avoid losing four straight starts for the first time since May 18-June 3, 2004 with Minnesota.
The Mets took a 2-0 lead in the first off Hudson, who was 6-0 with a 1.43 ERA in his previous eight starts.
In Denver, Chase Utley drove in six runs and hit a grand slam to cap a nine-run seventh inning as Philadelphia overcame a four-run deficit.
Utley’s six RBIs tied a career high and came after Ryan Howard and Jayson Werth also went deep during the big inning in which the Phillies had nine hits.
Antonio Bastardo (1-0) benefited from the Phillies’ big inning, getting the win despite allowing a run and four hits in one inning of relief. Brad Lidge got the last three outs for his 19th save but not before giving up a run.
Colorado had 19 hits.
Carlos Gonzalez hit his 31st homer and Chris Iannetta and Dexter Fowler also homered as the Rockies built a 7-3 lead heading into the seventh.
Manny Delcarmen (0-1), acquired from Boston earlier in the week, gave up four earned runs on four hits while getting just one out in his NL debut.
