Morton have already knocked the visitors out of the League Cup this season, but the home side's passage had been a relatively untroubled affair on that occasion. They were given an early sign that things might not be so straightforward this time as the underdogs claimed an early lead.
It was a spectacular effort, too, Scott Maxwell sending a fierce 18-yard shot high into the net after Colin Cameron's initial effort had been blocked. The visitors, though, were able to hold their advantage for just five minutes before Morton hit back with a slightly fortuitous goal.
McManus was the provider with a pinpoint cross which should have been converted by Stefan McCluskey; his miscue fell for sibling Jamie and he showed his younger brother how it should be done with an emphatic finish.
Morton took the lead when Jamie McCluskey's cross was met by Thomas O'Ware's towering header which flew into the net. The Greenock side looked content to hold on to their advantage during a scrappy second half though they might have made sure of victory when McManus had a shot cleared off the line.
Instead, a dramatic finale saw Craig Dargo upended in the home box in stoppage time and, although Lee Currie's spot kick was blocked by Caraux, the Berwick man followed-up to take the game into extra-time.
The match took another twist in the first period when Morton reclaimed the lead through a spectacular McManus shot - this time the visitors were broken, and McManus went on to add two more. Morton's night was slightly spoiled by a late red card for Jamie McCluskey.