Ryan Harpur's penalty 13 minutes into extra-time after a foul on Kris Lowe proves to be the winning goal for Dungannon.
Billy Joe Burns forced a superb save from Stuart Addis in extra-time.
Substitute Peter McMahon had equalised for Dungannon in the 85th minute, rifling the ball into the top corner to take the game into extra-time.
Colin Coates had made it 1-0 to Crusaders in the 49th minute with a glancing header into the top corner past Stuart Addis from Paul Heatley's free-kick.
In the first half, Coates had a header cleared off the line by Chris Hegarty and Heatley hit the bar with a drive.
Lowe fired a shot across the face of goal for Dungannon and in the second half Cormac Burke was just off-target with an effort.