Mooney, who leaves later this year to join professional Aussie Rules side Collingwood, showed what a loss he will be to Down football.
Brothers Ryan and Jerome Johnston and stoic defender Niall Donnelly also made a massive contribution to the Newry school’s 19th MacRory Cup title, and now they will go on to defend their Hogan Cup crown.
Mooney set the game alight with a 15th-minute screamer, blasted to the roof of the net from Jerome Johnston’s pass.
Four minutes later Harry Óg Conlan got in for a Dungannon goal but Newry, with Ryan Johnston revelling in his running midfield role, finished the first half with three points, two of them from Johnston, the other from Mooney.
The sides were level at the break on 1-4 each, but early in the second period, Dungannon eased two clear.
St Colman’s started to get on top at midfield and another flash of Mooney magic in the 43rd minute saw him rifle home another brilliant goal, this time following a move involving Johnston and skipper Connor Gough.
Jack Haughey and Patrick Morgan tagged on points to push them four clear but, once again, the academy hit back with a goal, finished with conviction by sub Aidan McGarrity.
In a thrilling finish, Shay McArdle and Ciaran Girvan swapped points, but St Colman’s held out for an 18th title, pulling further clear at the top of the Ulster colleges roll of honour.
Scorers for St Colman’s: C Mooney 2-2, J Johnston 0-4 (2f), S McArdle, J Haughey, P Morgan 0-1 each.
Scorers for St Patrick’s: H Óg Conlan, A McGarrity 1-0 each, L Girvan 0-4 (1f), S Quinn, D Quinn, K Morgan, R Devlin 0-1 each.
M McReynolds, J Carberry, S Molloy, M McAleer, E Deeney, S McGarrity, S Quinn, C McFall, P Barker, D Quin, K Morgan, H Og Conlan, Lavery, R Devlin, L Girvan.
Subs: A McGarrity for Barker, C Corrigan for McAleer, C Mallon for Morgan.
M McNeice, M O’Hare, N Donnelly, R Lively, D Brannigan, E Magee, K Haughey, R Johnston, C Gough, J Haughey, P Casey, C Mooney, S McArdle, J Johnston, T McGreevy.
Sub: P Morgan for O’Hare.
Referee: B Cassidy (Derry).