Hartlepool, 41 rungs below Stoke City, reached the fourth round of the competition for only the sixth time and beat a team from the top flight in the FA Cup for only the second.
A header from Michael Nelson four minutes after halftime and a second goal from substitute David Foley after 76 minutes left Stoke to concentrate on avoiding relegation during the second half of the season.
Stoke boss Tony Pulis told The Sentinel: "I am desperately disappointed to get beaten in the third round of the FA Cup. The game wasn’t a classic, but we knew it wasn’t going to be.
"Up until they got the goal, I thought we were OK. I couldn’t see them being a threat to be honest, but as soon as they scored the goal, they deserved to win the game from that point onwards.
"We made a lot of changes, but we still had players out on the pitch who I think are good enough to get us the result.
"One or two haven’t performed to their maximum, but you can’t take credit away from what Hartlepool have done. In the second half, they were better than us.
"It is probably my worst performance in the FA Cup as a manager. I think it is the first time I have gone down to a team lower down in the leagues and lost in the FA Cup."
Pulis has ordered the players in for training tomorrow. He said: "Against Manchester United and West Ham I don’t think our performances or the way we worked were that bad. But we imploded in those games.
"Today was totally different. It was a game when you wanted people to roll their sleeves up and battle and scrap for everything.
"But once they got the second goal, it gave them so much more impetus. It put about five yards on them, and we just couldn’t match it."