In a busy opening period, neither side could really establish an early foothold on the game.
Cliftonville went close midway through the half when Jonny Addis low free kick from just outside the penalty area brushed the outside of the side netting on its way past.
As the Reds began to gain some form of dominance, Rory Hale’s inch-perfect through ball sent Brian Healy clear of the Dungannon rearguard but Danny Wallace recovered superbly to poke the ball behind for a corner at full stretch.
Dungannon posed little threat to the Cliftonville goal in the opening 45 minutes with Gael Bigirimana’s long-range shot straight at Reds keeper PJ Morrison.
Dungannon’s first clear-cut opening of the game came just after the hour mark when Kealan Dillon’s pinpoint ball from midfield sent full-back Shea Gordon clear behind the Cliftonville defence but his shot lacked conviction and Morrison was able to save with his outstretched foot.
At the other end, Rory Hale created half a yard of space before finding Liam McStravick with a pass but the attacker’s tame shot was always straight at Declan Dunne.
Dungannon spurned another big opening late on as Gordon once again got himself into an advanced position and when his initial shocked was saved by Morrison, the ball bounced up but substitute Andrew Mkitchell could only loop his header onto the top of the net.
Dungannon enjoyed their best spell at the start of extra-time and were rewarded on 98 minutes when Mitchell cut the ball back from the right hand side of the penalty area into the path of the in-rushing Kealan Dillon who smashed a shot high into the net past Morrison.
Cliftonville had penalty appeals waved away in the second period of extra time after referee Morrison adjudged that Cahal McGinty had blocked Keevan Hawthorne’s low cross with his body rather than a hand.
But there was one final twist in stoppage time at the end of extra time as Hawthorne’s corner was bundled home at the near post via a combination of Joe Sheridan and defender Danny Wallace with what proved the last action of the game.
In the penalty shootout, Dungannon scored all four of their penalties while Sheridan saw his effort saved and Harry Wilson dragged his effort wide of the post.