It was the first walkoff win of the season for the Rockies.
''I think you've got to tip your hat to the Padres for how they battled back late in the game,'' Murphy said. ''But we had a really positive offensive ninth inning where I thought we grinded out some really good at bats.''
Trevor Story, Raimel Tapia and Garrett Hampson also hit run-scoring singles for Colorado, which blew a three-run lead in the eighth. Antonio Senzatela got a no-decision after pitching seven scoreless innings.
Jake Cronenworth hit a two-run double and Wil Myers had an RBI single during San Diego's three-run eighth that tied it at 3.
''They've got a good offensive team statistically across the board, so we know what we're up against with them,'' Colorado manager Bud Black said. ''We had them shut out through seven. We had two strikes and two outs on them a couple of different times (in the eighth) and we couldn't put them away.''
Senzatela bounced back from his last outing in which he allowed a career-high four home runs in an 11-3 loss to the Los Angeles Dodgers. He gave up seven hits, walked one and struck out three.
Daniel Bard (2-2) worked a scoreless ninth for the victory. Ryan McMahon started the Colorado ninth with a single up the middle off Craig Stammen (3-2). Hampson walked, and Josh Fuentes hit into a fielder's choice before Murphy lined sharply to left. It was the sixth career game-ending hit for Murphy.
''I thought we scattered some hits, ran into a couple outs on the bases, the double plays,'' San Diego manager Jayce Tingler said, referring to a pair of double plays the Rockies turned, including one by first baseman Ryan McMahon when he snared a line drive by Trent Grisham and quickly stepped on the bag to double off Luis Torrens in the fifth.
''If that ball gets down the line maybe we can get something going,'' Tingler said.
Left-hander Adrian Morejon was a late scratch as San Diego's starter and he was placed on the 10-day injured list. The team did not specify the reason for the move, and turned to a pitching by committee approach, starting with Michel Baez.
Trailing 3-0 going into their half of the eighth after coming up empty against Senzatela, the Padres got to reliever Carlos Estevez to even the score. Fernado Tatis Jr. walked and Manny Machado singled, extending his hitting streak to 11 games, ahead of Croneworth's two-out, two-run double. Myers followed with a run-scoring single.
Moving to bolster their bullpen, the Padres acquired RHP Trevor Rosenthal from Kansas City in exchange for OF Edward Olivares and a player to be named later. Rosenthal, who was the Royals' closer, had seven with a 3.29 ERA.
Padres: LHP Drew Pomeranz was reinstated from the 10-day injured list after recovering from a left should strain.
Rockies: RHP Chi Chi Gonzalez (right biceps tendinitis) has been reinstated from the 10-day injured list and RHP Ashton Goudeau was optioned to the team's alternate training site.
Padres: Chris Paddock (2-3, 5.15 ERA) is slated to make his first career start at Coors Field.
Rockies: RHP Ryan Castellani (1-1, 3.54 ERA), coming off his first career win Monday at Arizona, returns to the mound to make his fifth career start.
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