Town Boss Joe Royle admitted his side were poor in the first half, but was pleased with their comeback: "We were abysmal in the first half. I think it was our worst 45 minutes since we lost the first six games at the start of the season.
"I made changes because I had to. I know Shefki (Kuqi) was disappointed with the decision but Richard Naylor came on and gave us more.
"Martijn Reuser has been doing that all season for us. He scored a great free-kick, and then made the second and I thought we looked as if we were going to score a third.
"We want to get in to the play-offs, with three games left, but it's the players who have done it and that was our sixth win in seven games."
Meanwhile Royle revealed that Kelvin Davis did not take part because of a stomach bug: "Kelvin was getting paler and paler, so we sent him home to get him out of the way and avoid it spreading. Jermaine Wright was also affected for a couple of days."
Gillingham boss Andy Hessenthaler meanwhile felt that poor defending was to blame for his sides defeat: "It's not a nice thing to be in the bottom three. We played well in the first half, shutting them down, and perhaps we worked too hard, putting everything into it.
"We were 1-0 up at half-time but we didn't defend properly in the second half, certainly for their winning goal.
Gillingham 1-2 Ipswich - Manager Reaction
"That has been our problem all season, giving sloppy goals away. We've got big enough lads in there to defend that and the players involved will be disappointed because that's what they're there for. The lads had a free header and scored - game over.
"Once we went 2-1 down the confidence drained out of the side, the crowd got edgy, and it's difficult to come back after that.
"Our effort in the first half was fantastic, probably some of the best work we have put in all season, but we all ran out of steam in the second half.
"It's disappointing that we have dropped into the bottom three, there is only a point in it with three games left and we've got to win two out of three.
"We go to Wimbledon next week. They won again and seem to be playing with no fear now they know they are relegated. That won't make it any easier."