The Giants scored three runs in the seventh to tie the game, but left the bases loaded in the eighth and Scutaro got just enough of a 1-2 fastball from Santiago Casilla (0-2) to send it over the left field wall in the ninth.
Rex Brothers (2-2) pitched out of the bases-loaded jam in the eighth, striking out Brandon Belt and Melky Cabrera to end the inning and Rafael Betancourt fanned Nate Schierholtz with two aboard in the ninth to record his seventh save of the season.
Jeremy Guthrie returned from the disabled list and allowed one unearned run over 5 1/3 innings for the Rockies, who halted a four-game skid and earned a split of the series.
"Sometimes we pitch good and we don't hit, sometimes we hit good and we don't pitch. We just need to put those two things together and you're gonna see good results," said Scutaro.
Although Cabrera struck out to end the eighth, he helped tie the game an inning earlier when he hit a two-run double and later scored on Angel Pagan's two-out single.
Tim Lincecum gave up four runs in seven innings for the Giants, who saw their three-game win streak come to an end.
"It was one of those starts where he made some mistakes and didn't get away with them," Giants manager Bruce Bochy said of Lincecum. "But I see him getting better and better."
Josh Outman, who relieved Guthrie in the sixth, issued consecutive walks to start the seventh. Cabrera then slapped a two-run double into the right-field corner. Pagan's line drive single to left off of Matt Belisle brought around Cabrera, who slid in ahead of the throw for the tying run.
Brothers walked the bases loaded with one down in the eighth before retiring Belt and Cabrera. In the ninth, Pagan singled and Brandon Crawford walked with two down, but Schierholtz's bat didn't leave his shoulder as Betancourt delivered a 3-2, belt-high cutter across the middle of the plate for the game's final out.
Gregor Blanco scored the game's initial run. He led off with a single, stole second, moved to third on catcher Ramon Hernandez's throwing error and came home on Belt's sacrifice fly.
A half-inning later, Troy Tulowitzki singled on the heels of Carlos Gonzalez's double to make it 1-1.
In the sixth Tulowitzki singled again and advanced to third on an error by Pagan. A walk to Todd Helton preceded Michael Cuddyer's double to left, which plated Tulowitzki. Lincecum then walked Hernandez to load the bases and Jordan Pacheco delivered with a sac fly for a 3-1 Colorado lead.
The Rockies added to their advantage with a run in the seventh before relinquishing said advantage in the bottom half.
Tyler Colvin helped make it 4-1 when he singled, stole second, moved to third on a throwing error by catcher Buster Posey, then came home on Gonzalez's single.
Guthrie He was on the DL with an injured shoulder, which he suffered when he fell off of his bicycle...The Giants had won 10 of their previous 12 meetings with the Rockies dating back to last season...Giants infielder Joaquin Arias left the game with a forearm contusion.