With the score tied 6-6, Cuddyer (4-for-5, three runs scored) collected a one-out single and went to second on a sacrifice by pitcher Carlos Torres (1-0).
That brought up Pacheco (3-for-6, four RBI), who grounded an 0-1 pitch from Joe Thatcher (0-3) through the hole to chase home the go-ahead run.
Pacheco went to second on the throw and scored an insurance run when the next batter, Ramon Hernandez, also singled.
Torres earned the victory with two scoreless innings and Rafael Betancourt picked up his 16th save for the Rockies, who evened their three-game set.
Jesus Guzman went 2-for-3 with a solo homer, while Everth Cabrera added three hits and an RBI for the Padres.