Goals either side of half-time from captain Andy Nevin and Eoin McCormack on the famous Front Lawn rugby pitch in Blackrock sent shockwaves through the tournament.
Conor Foley's side had warmed up for the last-eight test of their credentials with a dramatic 4-3 victory over local rivals Marist College in the previous round.
Nevin, McCormack, Ian Rosney and Chris Regan were on target on that dramatic day as Marist three times came from behind to peg back Athlone, only for Regan to dramatically decide the tie late on.
The school that has never won this competition will now face the winners of Chanel College versus St Mary's DS, Drogheda in the semis.
Athlone are in fact the first team into the last four of the Senior Cup, with last year's beaten semi-finalists St Joseph's CBS, Farview, taking on St Colmchille's CS, Knocklyon, in their delayed quarter-final next month.
The final of the three outstanding last-eight ties will see Oatlands College welcome the winners of the last-16 encounter between St Peter's College, Dunboyne and St Paul's College, Raheny.
Both that third-round encounter and the quarter-final involving Oatlands and the winner are expected to be resolved in the first week back for schools.