Saints, the holders, missed the chance to go ahead two minutes into the third round tie, when Scott Preston’s penalty was saved by ’keeper Andy Slaughter.
Premier division champions Old Malton led 1-0 at half-time after Daman Cox’s 38th minute goal, but the first period was relatively even.
The hosts suffered a blow in the 55th minute when Simon Cooke was sent off for handling the ball on the goal line and Chris Hodgson despatched the penalty to level the scores.
Old Malton player-manager Darren Dunning came on to steady the ship with 20 minutes remaining.
The ten men were looking the more dangerous side and Danny Fogg bagged the winner with ten minutes remaining.
Terrington Glory reversed their home match with York St John University to ensure the game went ahead, but they were knocked out 5-4 on penalties.
In normal time Glory fought back from 3-1 down to force extra time and they again produced a comeback from 6-3 behind to level at 6-6.
Andy Park, Alex Yates and Jordan Grose all managed a brace of goals apiece for Terrington.
Meanwhile, torrential rain wiped out all of yesterday’s scheduled ties in the York FA Sunday Morning Senior Cup and the York FA Sunday Morning Junior Cup.