Pittsburgh snapped a six-game skid by handing Colorado a fourth straight loss.
Brubaker (4-4) allowed only two hits until the sixth inning, when Raimel Tapia had a leadoff single and C.J. Cron was hit by a pitch to load the bases with one out. Charlie Blackmon and Brendan Rodgers flied out to end the inning.
''I wanted it (the seventh inning), of course,'' Brubaker said. ''It's (manager Derek Shelton's) decision in the end. I told him I wanted it, but I knew his mind was made up. That was fine with me.''
The right-hander gave up four hits with five strikeouts before being relieved by Chasen Shreve in the seventh. Brubaker recovered from his previous two starts, when he allowed five runs in 5 2/3 innings against the St. Louis Cardinals on May 18 and surrendered seven in 5 1/3 to the Atlanta Braves five days later.
''He had given up some homers in the last few games,'' Shelton said. ''Just left some balls in the middle of the plate. ... He pitched to the edges. He used his breaking ball. He had one sequence where he came back and threw a 3-2 curveball after throwing two sliders. So I just think his mix and the execution of his mix was probably about as good as we've seen in the last three or four starts.''
Bryan Reynolds hit his team-leading sixth homer, a two-run shot to right that pushed the lead to 5-0 in the fifth, and Gregory Polanco scored on a fielder's choice, making it 6-0 later that inning. Polanco had a sacrifice fly an inning later.
Jon Gray (4-5) had his shortest outing in 11 starts for the Rockies this season, giving up three runs on four hits in three innings.
''I thought it started with the fastball,'' Colorado manager Bud Black said. ''Overall, it wasn't as crisp as we've seen it. The velocity and the control of it. I have to watch the video, but it looked as though there was a lot of horizontal movement, especially when he was trying to go into left-handers.''
Michael Perez got the Pirates going in a three-run second inning, driving in Wilmer Difo with a single back up the middle for a 1-0 lead. Brubaker walked, loading the bases with no outs.
Adam Frazier hit a potential double-play ball to first, but Cron's throw pulled Rodgers off second. Rodgers dove back to tag the base for one out, and Cole Tucker went home for a second run before Ben Gamel made it 3-0 with a sacrifice fly.
The doubleheader is the fifth for the Rockies this season and fourth in the past 26 games. They were swept in a twinbill Thursday by the Mets in New York.
Pittsburgh split its only previous doubleheader this season, beating the Tigers in the first game before dropping the second in Detroit on April 21.
Rockies: Trevor Story was placed on the 10-day injured list retroactive to May 28 with right elbow inflammation, stemming from a play in the second game of the doubleheader against the Mets on Thursday. The two-time All-Star shortstop left in the third inning after fielding a groundball from Cameron Maybin and making a spinning throw for the out at first. Black said an MRI has not been scheduled, but would take place Monday or Tuesday if there is one.
Pirates: OF Ka'ai Tom (wrist) was reinstated from the injured list and served as the 27th man on the roster for the doubleheader.
Right-hander Mitch Keller (2-6, 7.41 ERA) will take the mound for the Pirates against Rockies lefty Austin Gomber (3-4, 4.56) in the second game of the twin bill later Saturday.
On Sunday, Rockies LHP Kyle Freeland (0-0, 2.25) is expected to close out the three-game set against a pitcher yet to be announced by the Pirates. In his lone appearance this season, Freeland allowed one run on four hits in a 3-1 loss to the New York Mets on Tuesday.
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