The Mets secured their victory with a five-run second.
Omir Santos and Sullivan each had one RBI.
Like Berroa, Cory Sullivan had two hits and one RBI for the Mets, who can complete a four-game sweep by winning the nightcap.
Santana (12-8) surrendered four hits in seven innings with a walk and eight strikeouts.
Bobby Parnell and Tim Redding pitched the eighth and ninth, respectively.
Dexter Fowler, Troy Tulowitzki, reliever Josh Fogg and Todd Helton all had one hit for the Rockies, who have split their last six games.
The losing pitcher was starter Jason Hammel (5-6).
Wednesday's contest was the first rainout at Citi Field, New York's new home field.