The Potters gave a full debut to defender Ryan Shotton, whilst the inclusion of record signing Dave Kitson gave a possible hint towards the severity of James Beattie's injury. The £5m striker was the only member of last Saturdays squad to be included.
The Potters started by having to try and tame tricky winger Townsend, a player who caused them problems all night and Shotton, and later Griffin had their work cut out to contain the on loan Spurs player.
Kitson had two early chances but his first effort was deflected wide and his second, just a couple of minutes later was curled inches wide of the far post.
Orient then stepped up the tempo and took the game by the scruff of the neck. The Potters defence stood firm for the most of the onslaught but one effort that was allowed to get in struck the post from the dangerous Townsend after he was left alone at the back post.
The hosts had to change their keeper during the first period after Leon Cort had, purely by accident, clattered into him whilst trying to make contact with a dangerous corner.
Tom Soares, a player who looks desperately short of confidence, found Richard Cresswell shortly after and the striker pinged his effort across the keeper towards the far corner of the goal. The keeper had to throw himself to his right and just about managed to tip the ball around the far post and deny the ex-Leicester hitman his first goal since last seasons second round victory over Cheltenham.
The home sides star defender Ben Chorley was given the unenviable task of marking Kitson and he again let the ginger hitman turn away from him and get a shot in but the sub keeper got down and smothered the effort.
The second half started with 'The O's' on top and Patulea was given the simple task of nodding home from inside the 6-yard box but only managed to head the ball wide of the post.
Chances were few and far between but former club captain Andy Griffin and long term absentee Andrew Davies replaced Ibrahima Sonko and Ryan Shotton early in the second half. That left four subs all itching for their debut, 16-year-old keeper David Parton, 17-year-old striker Louis Moult and 18-year-old Nathaniel Wedderburn have all been produced via the clubs academy system and 18-year-old central midfielder Matthew Lund was signed from local rivals Crewe in the summer. It was Moult who got the nod shortly after the first two subs were introduced, coming on for Soares.
Moult looked nervous and started off, understandably, by keeping things simple and laying off the ball to the nearest man. The other thing to note, along with Moult's debut, was the booking of Leon Cort for a silly handball, the defender first caution since 2004.
The Potters pressed for a late winner, obviously not looking forward to another thirty minutes, and Pugh's corner was headed towards goal by Kitson. The ball was blocked and the rebound was struck by Tonge but another brave block scuppered the opportunity.
Kitson thought that long awaited moment had come when another Pugh corner was headed past the keeper by 'Big Dave' but the ball was headed onto the bar by Melligan, on the line, then bounced down back onto the defender head before cannoning up onto the bar again and away.
Moult was booked for a late tackle in front of the dugouts that had the majority of the 2,700 crowd baying for his dismissal as the 90 minutes came to an end.
The announcement that local car parks would be shutting their gates at 10pm had fans shuffling towards the exits as extra time started and they missed what should have been the opener as Townsend, again left unmarked, put a simple tap in wide. Stoke made the hosts pay as a corner was half cleared before falling to Kitson. He spun and hit the ball on the bounce with his weaker foot and the ball arrowed its way right into the top corner. Kitson stood arms aloft on the spot, 30 yards from goal, that he'd struck the effort as every outfield player raced over to congratulate the big man on his openign Potters effort.
Orient huffed and puffed but bar one excellent shot from 25 yards that Simonsen had to tip over they failed to threaten and the visitors comfortably saw out the remainder of extra time for a victory.