San Diego swept the three-game series and has won five of six. The Rockies have dropped five of six.
After reliever Roy Oswalt (0-5) walked home the tying run, Hundley hit a sharp grounder down the third-base line off Wilton Lopez to clear the bases.
Nick Vincent (4-2) pitched one inning for the win. Huston Street worked the ninth for his 29th save in 30 chances.
Oswalt allowed five runs on four hits with two walks in 3 1-3 innings in relief of starter Chad Bettis.
The 36-year-old Oswalt had been on the disabled list with a left hamstring strain for two months before being activated on Friday. The former 20-game winner was 0-4 with a 7.64 ERA in four starts this season with Colorado.
The Padres loaded the bases against Oswalt in the seventh on a leadoff walk to Chase Headley and consecutive singles by Kyle Blanks and Ronny Cedeno.
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After a short flyout, Oswalt walked pinch-hitter Jesus Guzman on four pitches to force in a run and tie it at 2. Lopez then relieved Oswalt to face Hundley.
The Rockies took a 1- lead in the third when Corey Dickerson tripled and Michael Cuddyer doubled.
Colorado added to its lead after Charlie Blackmon reached on a one-out error by shortstop Ronny Cedeno in the fourth and Jordan Pacheco followed with a run-scoring double.
Renee Rivera's sacrifice fly cut the lead to 2-1 in the fifth inning.
NOTES: Rockies CF Dexter Fowler (right knee strain) missed his second straight game. ... Despite being swept, Colorado won the season series against San Diego 12-7. ... The Rockies play at San Francisco on Monday night when RHP Jhoulys Chacin (13-8, 3.16 ERA) opposes RHP Tim Lincecum (9-13. 4.50). ... The Padres travel to Philadelphia and will open with RHP Andrew Cashner (8-8, 3.45) against RHP Tyler Cloyd (2-3, 3.57) on Monday night.
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