But the Giants battled back against Rafael Betancourt (1-2) in their last at-bat when Brandon Crawford drew a lead-off walk.
One out later, Pagan smashed a pitch off the base of the right-center field wall, which bounced away from Michael Cuddyer. Dexter Fowler picked it up and fired to Tulowitzki, but his relay to the plate was too late to catch Pagan.
Crawford went 2-for-3 with an RBI while Buster Posey added three hits for the Giants, who evened their three-game series.
Carlos Gonzalez went 3-for-5 with a solo homer for Colorado, which is grouped with San Francisco and Arizona atop the National League West.