Hartlepool's two late goals condemned York to their first defeat of 2014.
York missed a good chance to take the lead when Keith Lowe lifted the ball over the crossbar from six yards out.
Luke James opened the scoring on 82 minutes, firing in a low shot from the edge of the area after getting on the end of a Jack Baldwin knockdown.
And the lead was doubled when substitute Jack Barmby, the son of former England international Nicky, curled in a high shot on 89 minutes.
VIEW FROM THE DRESSING ROOM
York City manager Nigel Worthington told BBC Radio York:
"The performance for 82 minutes was very good. We were very strong, we were resilient, we competed and it was a good game overall.
"But the situation of how the first goal came about disappoints you from the point of view of indiscipline.
"That knocks the stuffing out of you and you're trying to get back in the game. Then they get a second because their tails are up.
"So it's there, you deal with it and because of the game on Tuesday night we've got to get ready to go for that."
Hartlepool United 01 Flinders 02 Austin 22 Holden 08 Walton 06 Baldwin 35 Burgess Booked 38 Walker Booked 18 Williams 09 Harewood (Franks - 69' ) 33 James 11 Monkhouse (Barmby - 79' ) Substitutes 05 Collins 07 Franks 12 Barmby 13 Rafferty 14 Compton 15 Sweeney 23 Rodney York City 31 Pope 02 Oyebanjo 03 Davies 10 Penn 15 Lowe Booked 05 McGurk 12 Carson Booked 14 Montrose Booked 19 Bowman (Jarvis - 30' ) 09 Fletcher 07 Coulson Substitutes 04 Smith 11 Jarvis (McCombe - 85' ) 16 McCombe 18 Platt 24 Ingham 25 Dickinson 37 Reed
Ref: Iain Williamson