The home side always had the edge, but were made to work by a City team determined to extend their nine-game unbeaten run away from home.
The game was a tremendous advert for League One football, and on this showing either of these sides - possibly even both of them - are good enough to make it to the promotion shake-up at the end of the season.
Pool took the lead with a penalty on 15 minutes, after Tony Butler was adjudged to have fouled Joel Porter, Butler booked for protesting over the decision.
After the fuss died down, Adam Boyd stepped up to slot home his 18th goal of the season from the spot.
Luke Wilkshire went close to equalizing with a long-range free-kick on 19 minutes, but City were level six minutes later when Steven Brooker got on the end of a long clearance, controlled it well and scored with a low angled shot into the corner after cutting inside from the left.
Pool were doing most of the pressing, and City keeper Steve Philips twice saved well from the nippy Porter.
It was closer in the second half, but Pool's hard work gave them the foundations to build on, and they took their match-winning lead on 71 minutes.
Porter and Boyd's neat passing up front opened up the City defence, and that allowed Tony Sweeney to power through from midfield to slot in his 11th goal of the season.
Pool had to fight hard to keep City out in a hectic final quarter, but with Mickey Nelson in brilliant form, the defence held out for their first win over City in 20 years.