Holders St Michael's of Enniskillen are out of the MacRory Cup as St Patrick's won a repeat of the 2012 final.
In a low-scoring quarter-final, Conor Carville's driving runs from the back helped the Maghera school ease ahead through Danny Tallon and Conor Murphy.
Jack McCann and Lee Brennan brought St Michael's level, before scores from Niall Toner and Peter Cassidy gave St Patrick's an 0-5 to 0-3 interval lead.
Cathal Mulholland and Daire Gallagher sealed the 0-7 to 0-5 victory.
Their late points came after two more Brennan efforts had brought the Fermanagh lads level.
An ugly brawl marred the end of the quarter-final win over Omagh at Emyvale where St Colman's, Newry, beat Omagh CNS 1-16 to 1-12.
St Colman's midfielder Conall Gough will miss the semi-final, after being sent off along with Colm O'Neill of Omagh.
Dara Noonan had just edged Newry into a two points lead when they were rocked by an Omagh blitz early in the second quarter.
Midfielder Brendan Donaghy charged through the middle for a brilliant solo goal, and two Ruairi Sludden scores edged them in front by three.
But St Colman's finished strongly, with two Jack Haughey frees and a punched goal from Noonan to go in at the break with a 1-8 to 1-5 lead.
Rice and Haughey helped St Colman's open an eight-point lead, and an Omagh revival which saw Sludden bring his tally to six, fell short.