Leaders Hartlepool ground out their latest win to extend their lead at the top of the Nationwide Division Three table to ten points.
Exeter’s determined defensive display looked to have foiled the home side, who were without their suspended top scorer Eifion Williams,after creating a bagful of chances.
But then two goals in a minute gave the leaders the edge and a penalty reply from Exeter was not enough to earn them the draw they felt they deserved.
Exeter keeper Kevin Miller was outstanding behind a hard-working City defence in a one-sided game, and his good saves mixed with some bad misses by the home attack combined to keep the score blank.
But Hartlepool at last came out on top in that late goals flurry.
They took the lead in the 78th minute when Richie Humphreys picked up a clearance on the edge of the area and side-stepped a defender before his shot was helped past Miller by a wicked deflection.
Within seconds it was 2-0 when Mark Tinkler chipped in a cross from the right for Adam Boyd, Williams’ replacement, to glance his header home from close range.
It looked all over, but Exeter had other ideas and James Coppinger ran at the home defence on the break yet again eight minutes from time, and at last got a reward.
He was brought down just inside the area by Graeme Lee, and substitute Justin Walker - who had only been on for a few minutes - slotted home the penalty.
But it was not enough to earn Exeter any reward for their hard work, and manager Neil McNab said: “I felt we were unlucky in some ways.
“The deflected goal was our undoing - without that we looked as if we were going to get something from the game.†Hartlepool boss Mike Newell said: “The result was a reward for our patience.
“Teams will always play well against the side at the top, and it’s happened again here.
“But we stuck at the job and got our reward in the end, though that late penalty made it more worrying than it should have been.â€