The next time up, Scutaro was prepared to do better.
Jonathan Herrera doubled with one out in the 11th off Stammen (3-1). After pinch-hitter Jason Giambi walked, Dexter Fowler hit a fly ball to deep center that was caught by Bryce Harper. Herrera tagged up and took third on the play, and pinch-runner Christian Friedrich later took second.
Scutaro was 13 for 68 (.191) with runners in scoring position when he came up against Stammen. Scutaro won it with a single in a seven pitch at-bat.
"Earlier I was a little more aggressive," Scutaro said. "Then when I got two strikes, I was trying pretty much to shorten my swing up and just try to make contact."
Adam Ottavino (2-0) pitched two scoreless innings and struck out five, including all three batters in the 11th.
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"I think I pitch better when the game's on the line," said Ottavino, who has 31 strikeouts and eight walks in 24 innings this season. "I just came in and wanted to throw up a zero. I knew we would score eventually."
Harper sent the game into extra innings when he led off the ninth with a homer, his eighth of the season, against Rafael Betancourt. The Colorado closer is 12 for 16 in save opportunities and has blown three of his past five chances.
Tyler Colvin had a career-high four hits, including a three-run homer in Colorado's five-run first, and set a career-best with five RBIs. Chris Nelson had an RBI double in the second and scored on Colvin's single to make it 7-0.
"We made it a lot harder on ourselves than we needed to," manager Jim Tracy said.
The Rockies went ahead in their half of the sixth against Tom Gorzelanny when they loaded the bases with no outs on two singles and a walk, and Gonzalez grounded into a double play.
For the second straight start, Josh Outman was staked to a big lead by the Rockies but was unable to pitch the five innings needed to qualify for a win on the 75-pitch limit Colorado is using for its four starters.
Outman, who lasted three innings and threw 67 pitches, took the mound in his final inning with the seven-run lead and gave up the five runs with two out.
Gonzalez had an RBI single and Nelson added a run-scoring infield single with the bases loaded in the five-run first against Edwin Jackson, with Gonzalez getting caught after rounding too far off third. Colvin then followed with his eighth homer of the season.
Jackson, left after yielding a leadoff single to Scutaro in the fourth, gave up season-highs in hits (10) and runs (8) in his shortest start since he lasted 2 1/3 innings at Coors Field on April 27, 2010.
"I feel the loss was on me," said Jackson, who is 0-1 with a 17.40 ERA in four starts at Coors Field. "Any time the bullpen has to come in in the fourth inning, it is not a great feeling when you are the starter that day."
- Morse left Wednesday night's game in the eighth with a tight right hamstring and stayed in the clubhouse late taking treatment. Nationals manager Davey Johnson was planning to sit Morse on Thursday but changed his mind when Morse said he was fine and able to play.
- Tracy said RF Michael Cuddyer was given a day to regroup. He entered the game in the 11th at first base. Cuddyer began the day with seven hits in his last 51 at-bats and was 2 for 12 in the first three games of the series. 1B Todd Helton hit fourth for the third time this season in Cuddyer's place, something he last did April 15, and Chris Nelson batted fifth for the first time this season.
- Rockies 3B Jordan Pacheco wasn't in the lineup due to soreness in his right quadriceps, which has bothered him off and on recently. He pinch hit in the ninth and had a sacrifice bunt.
- Jeff Francis (0-1) will start for the Rockies against the an Diego Padres on Friday. The Nationals will start Ross Detwiler (4-3) at Atlanta.