Jason Byrne struck for a late, late winner to give Bohemians a maiden Setanta Sports Cup win at The Oval.
In the battle of the league champions, Glentoran took the lead but the double winners showed their mettle by battling back to pick up a crucial win.
Glentoran were upset with learning of star striker Gary Hamilton and captain Paul Leeman's suspension at short notice, while Pat Fenlon left Gary Deegan, Paul Keegan, Glen Crowe and Byrne on the bench.
The Gypsies almost got the perfect start within the opening minute as Neale Fenn fired wide after good work from Anto Murphy, while Michael Halliday missed in similar circumstances at the other end five minutes in.
Making his debut for the Glens was Northern Ireland international Keith Gillespie and his corner found Johnny Taylor unmarked, but the centre half headed wide.
They should have gone in front 16 minutes in when Ken Oman clumsily fouled Shane McCabe in the area and David Malcolm pointed to the spot. But Bohs' stopper Brian Murphy wasn' t called into action as Richard Clarke sent the penalty over the bar.
The visitors grew into the game after surviving the scare and they could have been in front before the break as Paddy Madden drew a fine save from Elliott Morris with four minutes remaining.
And then Joseph Ndo went close with after his initial ball found Killian Brennan who took two attempts to find the Cameroon international in the box, but Taylor cleared off the line.
Scoreless at the break, it only took six minutes for the hosts to take the lead as Clarke and McCabe tried a one-two, but the second ball came to Waterworth and he took a touch before curling a low shot into the corner.
Pat Fenlon introduced Jason Byrne and Paul Keegan in response and it was a masterstroke with Keegan taking a free kick with his first touch and finding Byrne on the back post. The striker's effort was cleared by Halliday with Jason McGuinness lurking.
The centre half got his reward from the corner as Brennan's found him unmarked and he headed home.
Byrne's free kick drew a fine save from Morris before McGuinness’s header struck the upright as the Gypsies went in search for the winner.
And they left it late as Byrne pounced on McGuinness’s shot to turn it into the net and send the travelling fans into rapturous celebrations.
Glentoran: Morris; Nixon, Ward, Taylor, Hill; Keith Gillespie, McCabe, Clarke (Fitzgerald 65), Neill; Halliday, Hayworth.
Bohemians: Murphy; Brian Shelley, Oman, McGuinness, Powell, Murphy, Cronin (Keegan 61), Ndo, Brennan; Madden (J Byrne 61), Fenn (Crowe 68).
Referee: David Malcolm (Bangor)