With the Rockies trailing 2-1 after 5 1/2 innings, Dexter Fowler greeted Stephen Strasburg (9-2) with a leadoff triple in the sixth. After Strasburg hit Marco Scutaro with a pitch, Carlos Gonzalez chased home Fowler with a ground single to right field.
Pinch-runner Chris Nelson went to second on the play and to third on Michael Cuddyer's single before scoring the go-ahead run on Helton's deep fly to center.
Nelson went in to play second base and added an RBI single in the seventh for an insurance run as Colorado took the first of a four-game series.
The rally made a winner of Josh Roenicke (3-0), who tossed two scoreless innings in relief of starter Jeff Francis.
Strasburg's yielded three runs on six hits while striking out eight, and had a streak of six straight wins snapped.
Jesus Flores went 3-for-4 with two runs scored for the National League East-leading Nationals.