After winning against Plymouth at the weekend, Pools had to be patient at times against an opposition now winless in four, but they got on top and won it in the second half, leaving Cooper a happy manager.
He admitted: "The job was done. The same has to be said about Saturday. The difference between these two games and earlier in the season is that we seem to have found a way to get in front and stay in front.
"We have pasted teams without finding a finish - now by luck or judgement, we are in front, defending for our lives and finding something on the counter attack. The goals have come at good times for us."
Pools went in front on 32 minutes when Simon Walton scored from the penalty spot, but a Harry Pell spot-kick for the visitors on 66 minutes levelled the scores.
However, goals from Luke James and Matty Dolan secured all three points for the home team.
"I think if you look at both penalty incidents, they could go either way," added Cooper. "It's nice to see Matty Dolan and Simon on the scoresheet and Luke again when he had no right to.
"But when Wimbledon started loading our box, we had a goalkeeper coming to get the ball and two defenders in front of him who were winning headers.
"It was by no means perfect, and we can be so much better, but they are putting so much effort in to win games.
"It's a nice feeling to have, being confident. The mindset can shift quickly. You are used to losing, go behind and it's here we go again. Now we go in front, score, and it's here we go again.
"We can be so much better and raise standards and quality, but we are hard to break down and scoring nice goals."
Visiting boss Neal Ardley was furious with his side. He blasted defender Alan Bennett for conceding a penalty and then being beaten by James for the key second goal on 72 minutes.
"I'm really frustrated," he reflected. "We went behind to a goal that shouldn't have happened - if there's contact and Benno has brought him down in the box then it's absolute madness.
"He is going away from goal, going nowhere, it's a soft penalty. I wasn't happy with the referee and it sums it up that he's evened it up in the second half to get us back in the game.
"I'm furious with what's gone on for their second goal. A terrible goal to concede. We have done an 11 hour round-trip and go home with nothing. We worked ever so hard and at 1-1 there was only one team ever going to win it.
"But you ship goals at one end and you are fighting losing battles.
"Goals make the difference - simple isn't it. They defended their box, in and around it well, we didn't.
"It's an awful goal to give away their second. We gave the ball away and then showed poor, poor defending. The third goal - we are ending up chasing the game and they nick a third.
"We changed shaped to get back into it and the third is a killer, but it's poor defending that leads to it.
"We got back to 1-1 and I thought we would win it and then shot ourselves in the foot. I'm quite emotional and gutted about it. We did everything right leading up to it and threw it away with silly mistakes and lose 3-1 when it's never really a 3-1 if I'm honest."