Castletroy College and Midleton CBS filled the remaining two quarter-final spots as they saw off the challenge of De La Salle Waterford and Nenagh CBS respectively in the latest round of group games.
At Cashel, Castletroy went into their final clash with the 2007 and 2008 champions knowing that a victory was essential if they were to progress into the knockout stages.
They got off to a bad start, however, as Sean Hogan found the net for De La Salle and Billy O'Keeffe, Adam Farrell and David Walshe all pointed for the Waterford side.
An Ed Doyle kicked goal, augmented with points from Barry Nash and Tom Morrissey, helped Castletroy back into contention.
But at half-time, former champions De La Salle were still favourites to advance as they led by two points, Barry O'Mahony and Shane McNulty performing well for them.
The third quarter was where the game turned, however, as Castletroy managed an uninterrupted 1-4, John Fox scoring an excellent individual goal to get his side going.
While points from Austin Gleeson and O'Keeffe ensured that DLS were always in touch, Castletroy did enough to secure a famous 2-9 to 1-9 victory.
In the other game, at Charleville, Midleton CBS – who only needed a draw from their tie with reigning All-Ireland champions Nenagh CBS – looked to be heading out as the Tipperary school reeled off four unanswered points, two from Donncha Quinn and one each from Killian Gleeson and Andy Dunne, to lead by 1-11 to 0-13 as the game moved into injury-time.
An excellent point from the left sideline by Niall Motherway put Midleton back into second place in the table, however, and Billy Dunne then ensured victory by 0-15 to 1-11 and a spot in the last eight.
Nenagh had begun well and put down an early marker, Quinn notching a goal and a point to give them an early lead before centre-forward Tadhg Gallagher scored three fine points and put them back in the driving seat.
Frees from midfielder Joe Mellerick were keeping Midleton in the game, however.
Between the 20th and 55th minutes, Mellerick was his side's only scorer, notching nine points as the east Cork school moved into the lead, with Nenagh's attack beginning to struggle.
The late flurry looked to have been enough for Nenagh, but ultimately they were denied by a determined Midleton side, who move on to the quarter-finals.