The Rockies had won three straight, including the first two against the Pirates by twin 8-1 scores, but couldn't hold up in the tight game Sunday.
Harrison's sixth homer of the season was immediately followed by rookie Gregory Polanco's fifth homer in 40 games since his promotion to the Majors. The homers came off Brothers (3-5), who has struggled in tight situations this year after having a successful run as the team's closer last year.
"It's one that'll stick with me for awhile, but eventually I've got to turn the page and get on the plane for Chicago," Brothers said. "I'll continue to do what I do, good or bad, re-evaluate and see what I need to do tomorrow."
The loss left the Rockies 3-3 on their first homestand after the All-Star break. The stand included strong starting pitching from Jorge De La Rosa, Brett Anderson and Tyler Matzek. Also, Nolan Arenado homered Sunday for the second straight day and prevented a big third inning by snaring Pedro Alvarez's bases-loaded line drive and doubling Andrew McCutchen off third.
The Rockies will arrive in Chicago just a half-game better than the National League-worst Cubs, but the homestand was a boon to a club gradually getting back injured players.
"It was not bad," Arenado said. "If we'd won today we would have gone 4-2 on the homestand. We were able to split. That was cool. We won the series here, and we could take it into tomorrow."
In the sixth, Harrison created a 5-4 lead when he eluded much of the Rockies' defense to steal second and third on the same play.
Harrison beat catcher Wilin Rosario's throw to second but popped off the bag. Shortstop Josh Rutledge tagged Harrison while he was on the bag and believed he had him when he was off, but second-base umpire Chris Guccione didn't agree. With Harrison jogging toward third, Rutledge didn't give chase but flipped a throw to third baseman Arenado.
Harrison started back toward second, but Arenado threw too quickly, which allowed Harrison -- who escaped a similar rundown between second and third against the Mets exactly a month ago -- to change direction. Pitcher Tommy Kahnle and Rutledge exchanged throws but made the same mistake of not closing the distance or getting Harrison moving. Finally, Harrison slid under Rosario, a catcher out of his element on the infield dirt.
"It's just instinctive," Harrison said. "Rosario, he's a catcher and he's in his gear. He ran from home to third. My best chance was to try get a guy who was carrying an extra 15-20 pounds of gear. The move ended up working out."
It was a combination of a shifty player and poor execution.
"I look at a rundown as a free out," Rockies manager Walt Weiss said. "Harrison is probably one of the tougher guys to put away in a rundown but we've got to get the out there."
Kahnle would strike out Polanco and McCutchen, but Harrison scored on Ike Davis' pinch-hit double.
When Harrison eluded the Mets in the rundown on June 27, he won the game, 3-2, with a walkoff double in the 11th. He would repeat his game-winning form Sunday.
Arenado tied it in the bottom of the seventh with a home run to dead-center off Pirates reliever Tony Watson (7-1). But Brothers' struggles negated a chance at victory, although the eighth had a Rockies highlight. Carlos Gonzalez, who didn't start because of a twisted right ankle he sustained Saturday afternoon at home, made a full-length dive to rob Neil Walker of extra bases on a drive to the right-field corner.
Gonzalez had to play defense in pain in the late innings because Barnes was slowed because his right hamstring hurt while stretching before the game, Corey Dickerson is playing with a left groin strain and Drew Stubbs turned his left foot hitting a homer Friday..
The wild late innings came after tedious work from both starting pitchers. The Rockies' Franklin Morales gave up just two runs but left after completing four innings and facing three batters in the fifth. He gave up six hits and five walks, against three strikeouts.
Morales, however, could say he outpitched Pirates starter Edinson Volquez, who yielded four runs, two earned, in 4 1/3 innings. The Rockies had bases loaded when Volquez came out in the fifth. But reliever Jared Hughes forced Brandon Barnes -- who had already hit his fifth homer of the season, for two runs off Volquez in the fourth -- into an inning-ending double play.
Rockies reliever Chad Bettis' struggles continued in the sixth, when he gave up a two-run, pinch-hit homer to Travis Snider -- his sixth of the season -- and a total of three runs on four hits to lift his ERA to 9.38.
In the eighth with Watson pitching, DJ LeMahieu tried to steal third on a high fastball and was caught, ending the rally. Mark Melancon earned his 19th save.