Tom Bayliss, who came on as a second-half substitute, finished calmly past Jamie Cumming to make it three wins in three.
It was a game where the hosts had the majority of the possession, but clear-cut chances were few and far between.
And Town went on to win it in the 89th minute when Bayliss capitalised on an MK Dons mistake.
The boss was delighted with the result, and he hailed the players' togetherness after an honest display.
He said: "I said to them in there, coming together is the beginning of things. And then keeping together will get you to progress. And then working together will get you success.
"Oddly, it’s the bit in the middle that trips you up, the keeping together - if you haven’t got a team spirit.
"And that’s why we won the game tonight – because those boys in there are keeping together, and they don’t give in when they are tired.
"I’ve just said to the boys in there – there are many ways to win a football match.
"You can have possession, not so much possession, defensively, all-out attack, counter-attack – there are lots of ways you can win a football match.
"They may be down in the lower parts of the league, but they have got a really, really, good squad.
"They will be buoyed by the victory they had at the weekend so it was going to be one of those tricky games coming here.
"It’s a big old pitch. I think our squad have done incredibly well now – over 27 games – to be still running and putting the energy they have put in to a game.
"We travelled down today. It's been a hard shift for them.
I just felt at half-time, the little bit of change of shape was better for us – certainly the way the game was going.
"I thought they had control of the middle of the park in the first half. They didn’t have so much control of the middle of the park in the second half.
"And then if we are going to get an opportunity in that area, I don’t mind Tom Bayliss on it because his technique is probably Premier League.
"Taylor Moore said in the dressing room, jokingly, he put him a little bit too wide because he thought he was going to cut it back for him to score. Thank god he never!
"A lot has been said about our boys. But those things I’ve mentioned there, they are the bits that keep them going.
"It was a really, really, tough, hard, honest, three-points we got tonight."