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Justin Edinburgh saluted the finishing of matchwinner Rory Donnelly but admitted he nearly subbed him.
Donnelly scored with a 92nd-minute strike to hand the Gills a 1-0 win over bottom club Crewe.
Gills boss Edinburgh said: “It wasn’t his best game but you want to keep your form players on the pitch. It paid off.
“It was a sublime finish and a great time to score. There was no coming back from that.”
Edinburgh withdrew Bradley Garmston instead of Donnelly as the left-back was struggling with cramp.
Edinburgh said: “The change was enforced in the end. We may have made a change (for Donnelly) and played Brennan higher up the pitch but Bradley Garmston had a bit of cramp. Things like that happen.
“With it being late we were always likely to leave him on because of what he can produce and that certainly happened.”
The Gills manager felt his side were worthy of the win, in the end.
“We grew into the game,” he said.
“We weren’t as good as I would have wanted us to be first half, we were a little slow in our passing and closing down, but credit to the players, they picked up the pace of the game second half.
“We had enough chances to win the game but what a goal it was to win us the three points.”