Fraser Mullen had given the Blue Brazil a first-half lead after a strong start, only for Kieran Gibbons to net Kilby’s equaliser in the second-half. Following a goal-less first-leg, the match went through 30 minutes of extra-time before penalties.
The Fife side had been dismal from the spot, having missed several throughout the season, including one in the first-leg. However, they netted all five spot-kicks with Liam Henderson scoring the winner.
Keeping their League Two place allows Cowden to rebuild having replaced Liam Fox with Gary Locke and Billy Brown, who had missed the first-half due to a delayed flight from Magaluf, in March. The duo prevented three successive relegations.
East Kilbride will have to go again having romped to Lowland League success before seeing off Highland League outfit Brora Rangers to set up the play-off clash.