Trailing 2-0 from the first leg they knew they had to win 3-0 at Harlequin Park to qualify for the tournament.
And it looked like they were going to do so until, with three minutes left, Railway scored to progress on the away goals rule.
Little wonder the Harlequins players were so distraught at the final whistle - they had produced some top-class hockey to lead by three clear goals.
Indeed Railway had keeper Jane Coyne to thank that the gap wasn’t greater, as she made a series of saves from Karen Bateman, Emer Dillon and Rachel Kohler.
The Cork side grabbed the lead their approach play deserved after 23 minutes when Jane Chapple was on target after some good work by Dillon and Bateman.
Two goals in two minutes saw them lead 3-0 at half-time, with Karen Bateman scoring from a short corner and Chapple getting her second of the day after Jayne O’Brien played her though.
Harlequins continued to dominate after the break, with Julia O’Halloran, Bateman and Marissa Ahern all unlucky not to score.
But as the game went on Railway came more into it and with five minutes left they won a series of short corners with Harlequins keeper Orla McCarthy saving well from Ciara O’Brien and Marisa Ahern blocking superbly, also from O’Brien.
But, just as Quins seemed to have weathered the storm, Railway got another corner and Karen Clarke was on hand to tap home and send Harlequins crashing out of the competition.
There was no such drama for Cork Church of Ireland, as they crashed out 10-1 on aggregate to Pegasus, losing 5-1 on Saturday.
In men’s hockey, the brilliance of goalkeeper Wesley Bateman and their ability to convert penalty corners into goals were two of the main factors in Cork Harlequins’ 5-1 win over Glenanne in their second leg quarter-final match in the All-Ireland Club Championship at Harlequin Park on Saturday.
In a tough, an uncompromising contest, Bateman showed why he is rated one of the top goalkeepers in the country as he brought off at least six outstanding saves in an opening half which saw Glenanne exert a lot of first half pressure but still found themselves 3-1 down at the interval.
Harlequins had opened the scoring in the 14th minute through John Hobbs and while Paul Fitzpatrick equalised for Glenanne from a 21st minute penalty corner, two David Eakins dragged flicked goals from penalty corners in the 24th and 33 minutes sent the home side in with a comfortable lead at the break.
Harlequins always held the upper hand in a tough second half and finished with a flourish, with John Hobbs adding two more goals from penalty corners in the 65th and 67th minutes to complete a fine win and ensure their place in next weekend’s finals at Garryduff.
Joining Cork Harlequins in the finals will be Irish Senior Cup holders Lisnagarvey,who played out a ten goal thriller with Pembroke Wanderers at Serpentine Avenue in Dublin.
The sides finished level 5-5 and 7-7 on aggregate with Lisnagarvey qualifying on the away goals rule.
As expected, Annadale, who had a 6-0 first leg win over Cork Church of Ireland, have also made it to the finals. Goals from Graham Shaw, Iain Lewers and Chris Jackson gave them a 3-0 win at Lough Moss.
The fourth team in the Club Championship finals will be Aer Lingus who gained a2-2 draw with Banbridge at Havelock Park to win the tie overall 6-4.