Ivorian striker Armand Gnanduillet and Jack Lester finally broke Wimbledon's resistance in the second half to leave the visitors at the bottom of League Two.
Cook said: "It was a game that if we hadn't had won, I'm not saying our season would have been over but it would have been a challenge to get into the play-offs.
"Every point is vital and I told the lads at half-time, this is our season here in the second half and we will not get this back.
"We had to remain patient, strong and believe in what we were doing and to a man I felt we did that.
"I thought the lads gave a great response. We were dogged, we defended well when we had to and when we counter-attacked, we looked a threat and that was pleasing for me as a manager."