Stoch scored 262.7 points from his two jumps on the large hill at Kuopio, beating Severin Freund of Germany in second place with 258.9 points. Norway's Anders Bardal was third with 257.6.
The win gave Stoch 1,231 points in the overall standings, ahead of Slovenia's Peter Prevc with 1,128 and Freund with 987.
Stoch, who was leading the standings before the Sochi Olympics, was briefly pushed down to second place on Friday by Prevc until he regained the lead in Lahti, Finland, on Sunday.
Prevc finished fourth on Tuesday.
Stoch won both the large and small hill Olympic titles at Sochi, becoming only the third jumper—after Simon Amman and Matti Nykanen—to win double jumping golds in the same Winter Games.