"You're never happy with the way this ended here," Nelson said. "We don't play defense like that. We don't leave runners in scoring position the way we did today."
The Rockies were 2-for-9 with runners in scoring postion in the nightcap, and 2-for-11 in the first game.
The error total was one shy of the club record, set June 4, 1996, at Houston.
"We lost the game defensively," Rockies manager Jim Tracy said. "We gave them four runs that they would not have had.
"It's young people that if they're going to learn, they're not going to learn a lot in a 9-1 game or a 13-2 game. But hopefully they understand the importance of execution in close ballgames."
Nelson's three-run shot off Phillies starter Travis Cloyd in the third, his eighth homer of the season, gave the Rockies a 4-1 lead. However, the Rockies could not score again or hold the lead.
Rockies starter Drew Pomeranz had an inefficient performance. He gave up just one run and four hits in four innings, but left the game because he had 77 pitches by then. Since June the Rockies have been limiting starters to around 75 pitches, which coincides with the more-important benchmark of not letting them face a lineup a third time. Hitters have a .297 average against Pomeranz, for example, in the third plate appearance.
"I felt good out there, felt like I was throwing all my pitches for strikes," Pomeranz said. "We all know going out there what we have that day. When he [Tracy] tells me I'm done, I'm done."
Pomeranz has pitched as many as five innings just once in his last eight starts, but Tracy saw his work Sunday as generally positive.
"He did a good job early in the count, but then it took pitches to try to put hitters away," Tracy said. "But he didn't pitch badly."
But by game's end the pitching didn't matter because the Rockies' defense was so poor.
Colorado's lead began slipping away in the fifth with Josh Roenicke (4-2) on the mound. Nelson's second error, which came when John Mayberry Jr.'s grounder bounced off him, set up Chase Utley's single. Herrera missed Roenicke's pickoff throw, which might have beaten Mayberry, to put runners at second and third. Ryan Howard's two-run single made it a one-run game.
Ty Wigginton, a Rockie last year, opened the sixth with a game-tying homer. The Phillies had three one-out singles, the last being Kevin Fransden's infield roller to Nelson with runners at first and third to plate the go-ahead run.
Herrera booted Michael Martinez's two-out grounder, and the Phillies extended their lead with singles off Will Harris by Carlos Ruiz and Nate Schierholtz.
The teams used 13 pitchers. The Phillies' B.J. Rosenberg (1-2) earned the decision with a perfect, two-strikeout sixth, and Jonathan Papelbon -- the winner in the first two games of the series -- converted his 32nd save.
Thanks in part to the Rockies' miscues over the weekend and to their own opportunistic play, the Phillies (69-71) have recovered from a series of crippling injuries to find themselves on the outskirts of the National League Wild Card chase.
"Teams do pack [it] in, but at same time, I do know our guys and they're not going to pack it in," Phillies manager Charlie Manuel said. "They play hard. I've got to give them a lot of credit for that.
"Just keep winning. Only way we can win is keep going."