The loss was the fourth in a row for the reeling D-backs, who are now 2-15 at home and a Majors-worst 8-22 overall.
The D-backs had rallied to tie the game in the eighth when A.J. Pollock hit a two-out home run that hit the foul pole in left.
Reed, though, could not hold the Rockies in check.
He started off the ninth inning by jumping ahead of Drew Stubbs 0-2.
"Got 0-2 quick," Reed said. "I was feeling good."
Stubbs then laid off two fastballs that were called balls and Reed decided to go with a slider.
"Terrible slider in the zone," Reed said. "It was supposed to be down and away, left it out over the middle of the plate and he made me pay for it."
Stubbs drove the pitch the opposite way and over the wall for what proved to be the game winner.
"I was just trying to battle," Stubbs said. "He left a slider out over the middle of the plate. I was looking to go the other way. It worked out. I faced him a couple of times last year. It helps when you've faced a guy before. You know their tendencies. You know how they're going to attack you a little bit."
Reed fell to 0-2 while Boone Logan (1-0) picked up the win.
The D-backs could have given the pitching staff more breathing room had they been able to cash in more of their scoring opportunities.
"We had a ton of opportunities," D-backs manager Kirk Gibson said. "We were 1-for-9 with runners in scoring position. We left 11 guys on. Regardless, we had our opportunities. The guys battled their tails off tonight."
The inning that will no doubt stick out when the D-backs look back on the game was in the sixth when they had the bases loaded with nobody out.
Rockies starter Tyler Chatwood was removed at that point due to stiffness in his right elbow and Walt Weiss turned to Chris Martin.
Martin got Chris Owings to ground sharply to third and the Rockies were able to get the lead runner at home.
So with one out and the bases still loaded and both Martin Prado and Cody Ross available on the bench, Gibson decided to send up Roger Kieschnick to hit for pitcher Joe Thatcher.
Kieschnick struck out -- his fifth in seven at-bats this year -- and Tony Campana grounded out to first to end the threat.
"I considered it," Gibson said when asked about hitting Ross or Prado in that situation rather than Kieschnick. "But where we were at and knowing the guys that we had on the bench, that we'd be coming around again. And actually when we came around again we had those guys in there and it worked fine. You have to make your choices and I thought it was a pretty good matchup for Roger, actually."
Mike Bolsinger, making his third big league start, took a 3-2 lead into the sixth and had done a nice job of holding the Rockies in check.
But in the span of two batters, it all disappeared.
Carlos Gonzalez led off with a double and Troy Tulowitzki followed with a homer to right-center to give the Rockies their first lead of the game.
"You look at that lineup, and it's a good hitting lineup," Bolsinger said. "You've really got to work, and if you make a mistake, I made a mistake to Tulo and he hit a home run. You've just got to have better pitch selection."