James Morrison opened the scoring, blasting the ball at goal from distance and his swerving effort avoided keeper Thomas Sorenson who should have made an easy save.
Substitute Cameron Jerome gave the home fans some respite after heading in Jermaine Pennant’s free-kick, but the balance didn’t last long as Graham Dorrans was handed a set-piece of his own that flew between attackers and defenders alike before crashing into the back of Sorenson’s net.
On the victory Hodgson told reporters: “I’m very pleased with the result, pleased with the performance, pleased with the travelling support; I thought they were excellent, so a very satisfying day.
“When you lead for so long and you survive the penalty where your goalkeeper has made a great save, when it gets that close to the end you hope that it’s going to lead to three points.
“When that goal goes in [Stoke’s equaliser] you realise it’s not going to be three points or there’s a good chance it’s not going to be three points, and furthermore the team that has that late goal often has that initiative and go and get a second one.
"But, I think it was very strong of our team to come back and get the winning goal themselves when most people would have had Stoke down as the team with impetus.”
Jonathan Walters had a perfect chance 20 minutes from time to bring Stoke back in the game with a penalty that looked as though was undeserved, but the striker failed to make the opportunity count as Ben Foster saved his effort impressively.
“I’ve seen it in slow-motion, I’ve seen it as a replay, looks like a very harsh decision,” Hodgson said of the spot-kick.
On the many changes he was forced to make, Hodgson added: “Well the depth of this squad is as strong as it is.
“[Today] we haven’t played with [Shane] Long, [Peter] Odemwingie and in normal circumstances that’s a lot of players to be missing from what people consider to be your first eleven and yet the players have come and done a fantastic job and we end up getting a result here at Stoke which the club have been waiting for 30 years.”
Quizzed on the team’s ailing home form, he said: “The missed opportunities at home are being in some way compensated by some excellent performances in the away results. If we’d have done better at home then we’d be well over 30 points and we’d be turning cartwheels. We’re still a long way away, our target is 40 points like a large percentage of teams in this league.”
Meanwhile, Stoke boss Tony Pulis was left disappointed by his side’s display and bemoaned the lack of activity during the game from his players.
He told reporters: “I thought it was a pretty flat performance from us, especially first-half, I thought we were very, very flat. We’ve been on a great run lately and for some reason we started the game very flat.
“The two goals we’ve conceded are very disappointing from our point of view, they had very good opportunities and they rattled the bar a few times.
“They played five in midfield which two or three teams have come to our place and just sat in there and broke well. Second-half we stepped it up a little bit, obviously the penalty miss is a disappointment, with 20 minutes to go.”
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