Quakers were in control of the game at the Travelworld Arena, after goals by Liam Hardy and Nathan Cartman put them 2-0 up, but after pulling a goal back before half time, Marine scored twice in the last ten minutes to go through to the next round.
Quakers put Marine under immediate pressure , and in the opening 30 seconds Liam Hardy turned well inside the box, but his left foot shot was blocked.
On 6 minutes Josh Gillies did well to find Terry Galbraith on the left, and the full back whipped a dangerous cross in to the near post that a defender put behind just ahead of Nathan Cartman.
Marine had a great chance in their first attack, when Obi Anoruo broke down the right and crossed low into the middle for Michael Monaghan to fire towards goal, but Ben Dudzinski saved well.
Quakers responded with a corner from the right by Terry Galbraith that Gary Brown headed through a crowd of players at Calvin Hare.
Quakers went in front on 13 minutes when Galbraith burst into the box down the left and pulled the ball back perfectly for Liam Hardy to sidefoot in his 8th goal of the season.
Quakers nearly made it 2-0 on 17 minutes when Leon Scott made a good run forward, played a 1-2 with Gillies, and Hare saved his low shot down to his right.
But Dudzinski had to be alert to make another save on on 23 minutes when Warren Bellew cut in from the left and hit a low shot that the keeper saved at full stretch,and on the half hour Anoruo broke clear, but sidefooted wide of the right hand post.
Quakers went 2-0 up on 35 minutes when Gary Brown perfectly weighted a 40 yard pass over the top of the Marine defence for Nathan Cartman to sneak onto and half volley past Hare.
But Marine pulled a goal back inside a minute, when a free kick was driven into the Darlington box from the right,and Anoruo scored at the second attempt.
Half time Marine 1 Darlington 2
The referee, Simon Mather, turned down loud penalty appeals for handball at the start of the second half when Marrs blocked a shot by Bellew, and gave a corner instead.
Marine nearly levelled on 62 minutes. Falkingham and Brown were both yellow carded for fouls, and when the free kick was floated in, Adam Hughes headed across Dudzinski but also past the post.
Quakers responded with a low shot from an acute angle by Cartman that went wide, then Brown headed a Gillies corner on to the roof of the net
Quakers tried to kill the game, but Marine got back into it on 81 minutes when Danny Mitchley picked the ball up in space 30 yards out, and curled a right foot shot out of Dudzinski’s reach into the top right corner.
And in the fifth minute of stoppage time, Hunter was adjudged to have pushed James Foley although there seemed to be little contact and Mitchley buried the penalty.
Manager Martin Gray said; “At 2-0 up, we were comfortable, but after that indiscipline cost us. We gave silly free kicks away, and didn’t defend setpieces well at all. That has become a real concern, and things will change.
“Whether it was a penalty or not, things happened leading up to it that should have been prevented.
Dudzinski, Marrs, Galbraith, Falkingham (sub Beck 61), Hunter, Brown, Syers, Scott, Hardy (sub Thompson 63), Cartman (sub Turnbull) 70, Gillies
Subs; Bell, Milburn
Booking: Marrs, Falkingham, Hunter
Marine: Hare, Field, Short, Brizzell, Foley, Hughes, Monaghan, Smart, Mitchley, Anoruo, Bellew
Subs: Horgan, Myler, Hessey, Moore, Porter