The 34-year-old former Crystal Palace and Birmingham forward sealed the points for the U's three minutes from time after Sanchez Watt had ended his goal-drought soon after half-time - his first goal since October 2012.
There was still time for substitute Freddie Sears to add a third in the dying moments, but Dunne revealed it was Morrison's effort that pleased him most.
"Special praise goes to Clinton Morrison - Jabo (Ibhere) pulled out at 1.30pm, I spoke to Clinton, who said he could give me 60 or 70 minutes," said Dunne.
"He went even longer, his hold-up play was exceptional and I was delighted he scored.
"I think it was one of the best performances of my managerial career. That's how we want to play.
"I think the key moment was in the first half. We were passing the ball around the back and there was a lot of encouragement.
"We did that previously against Crewe, and there was a bit of nervousness about the crowd. Everybody was behind the team, and we were excellent from start to finish.
"We never took our foot off the gas. We constantly created chances, and sometimes you think that's best to keep it tight at the back. But we kept on going."
It could have been more for Colchester, but Gills goalkeeper Stuart Nelson denied Luke Garbutt on several occasions, while Brian Wilson saw his effort cleared off the goal-line by Leon Legge
Cody McDonald had Gillingham's best chance in the first half with a 20-yard effort that went narrowly wide, while Danny Kedwell headed over the crossbar from Jake Hessenthaler's corner.
- Sports & Recreation
- Clinton Morrison
- Sanchez Watt