Bolton boss Dougie Freedman criticised his team for not taking their chances as Michael Chopra's last gasp goal gave Ipswich victory at the Reebok.
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Wanderers got off to a flyer as Mark Davies's 30-yard effort flew past Stephen Henderson into the roof of the net from 30 yards just six minutes into the game.
But the Trotters failed to add to their lead and Daryl Murphy won a penalty with 20 minutes to go, giving DJ Campbell the chance to draw the game level from the spot.
Campbell coolly slotted home for his seventh of the season, and, in the 90th minute, Murphy's long range shot was too much to handle for Adam Bogdan, who could only parry the ball into the path of Chopra.
The former Cardiff and Sunderland marksman scrambled the ball in from close range to inflict on Freedman his first defeat since he took charge.
"Ipswich thoroughly deserved to win the match and we've got no complaints," Freedman said.
"I felt for 70 minutes we played very well and were the better team because we were creating opportunities. We probably actually did enough to win the match.
"We didn't take those chances though, and in the last 15 minutes we were a bit edgy.
"That gave them the impetus and the chance to make us pay and they did that to us in the end.
Speaking about the performance of goalkeeper Bogdan, Freedman added: "In football there are so many ups and downs and Adam has had so many of those ups recently.
"It was a difficult shot to stop and I thought that he was one of our better players overall and I think the message is that we've got to see our games out."
The Tractor Boys have now won four out of seven since the appointment of Mick McCarthy.
It was also the first time the club have recorded back-to-back league victories since March and they are now five points clear of the relegation zone.
"I'm delighted with the win and I really wanted to win this game," said McCarthy.
"I thought that it was fairly even throughout and in the end that the three substitutes we brought on won it for us.
"It's really clichéd but you've just got to take it one game at a time.
"There is a good spirit here now which wasn't here when I first came.
"There was a lot of finger pointing then but now we all seem to be pushing in the right direction.
"We're nowhere near to safety just yet though, and we just need to keep looking to pick up maximum points.
"I was really pleased for Michael (Chopra) because he has had some tough times.
"It was a great striker's goal and after all the hard work that he puts in he really deserved it."