Michael Woods repeated his winner at Bootham Crescent in August when he scored the vital goal in Hartlepool United's victory over York City.
Nathan Thomas put Pools ahead in the 24th minute and the job looked easier for the home side when York went down to 10 men on 35 minutes when Dave Winfield was sent off.
But Kyle Cameron headed the Minstermen level at the end of the first half.
Pools did not hit any heights in the second half but Woods came up with the goods 18 minutes from time following Carl Magnay's cross from the right.
Pools made a good opening with Thomas the brightest player on the park.
He also had a couple of cracks at goal, shooting over and having am effort saved by Flinders.
Pools put together one of the best moves of the half in the 18th minute with Bates, Featherston, Hawkins and Thomas combining before James had his shot blocked.
But Pools did not have long to wait for a goal with THOMAS scoring his fifth of the season since joining the club.
Hawkins' corner was not the prettiest but found its way to Thomas who finished neatly into Flinders' bottom-left corner
Thomas dedicated the goal to his late grandad but was booked by referee Seb Stockbridge for removing his jersey.
The referee had his yellow card out again 10 minutes from the interval when Dave Winfield needlessly brought down Thomas.
Having already been booked for a bad tackle on Thom as, the centre-half was off.
Flinders then kept his side in it with two saves from Duckworth, the first with his feet and the second a diving stop to his left.
But just when Pools thought they were going into the break one up, York levelled in the opening seconds of added time.
Luke Summerfield's corner from the left was headed in by the unmarked CAMERON from 12 yards,
Pools were flat at the start of the second half but at last put a move together in the 56th minute.
It ended with Duckworth being flagged offside though he had missed with his shot anyway .
Pools finally had an effort on goal on the hour when Woods had a shot from a Hawkins pull-back saved by Flinders.
And there was another effort two minutes later, when a diving James header wide from Magnay's cross went wide.
Flinders came to City's rescue on 66 minutes with a great save from Woods after a James knockdown.
But the goal finally arrived in the 72nd minute as WOODS scored for the second Saturday in arow.
Pools showed patience in possession and it was rewarded when Magnay had space and time to cross and his delivery was put in at the back post by Woods who had scored in the win
at Bootham Crescent.
The game was not won and it needed a vital save by Carson from Hendrie after good play by the ex-Pools loanee.
There was almost a third when a brilliant piece of James skill on the edge of the box was matched by an equally brilliant Flinders save.
Pools: Carson, Magnay, Bates, Jackson, Carroll (Richards 76), Featherstone, Hawkins, Woods, Duckworth (Blackford 84), James, Thomas (Oates 69).
Subs: Bartlett, Richards, Laurent, Walker, Bingham, Oates, Blackford.
Goal: Thomas 24, Woods 72
Booked: Thomas 25
York City: Flinders, Hendrie, Winfield, Bennett, Cameron, Dixon (Gilbraith 75), Summerfield, Penn, Allesandra, Oliver (Ilesanmi 37), Fewster (Riordan 82)
Subs: Ingham,, Carson, Riordon, Thompson, McEvoy, Gilbraith
Goal: Cameron 45
Booked: Winfield 19, Dixon 29
Sent-off: Winfield 35
Referee: Seb Stockbridge
Att: 4,781 (York 527)