
Argyle led 1-0 at half-time after an early goal from defender Alex Mitchell and had the chances to have been further ahead, and probably out of sight, by half-time.
However, they could not add to their tally before the break and then Wimbledon equalised early in the second half with a close range finish from Alistair Smith.
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Wimbledon, desperate for points in their fight against relegation, briefly threatened to turn the game around in their favour.
Cleverley responded by making a double substitution with Bim Pepple and Matty Sorinola sent on and Argyle went on to regain control of the game with goals from Lorent Tolaj and Pepple.
Argyle moved up to seventh position, two points away from the top six spot they are chasing, after their 11th away league win of the campaign.
Cleverley said: "First of all, huge result. I thought the players delivered the fundamentals really well. You have got to run, you have got to compete, you have got to duel, you have got to do your job at set plays to give you a foundation of being hard to beat in the game and I thought we did that.
"We created a lot of turnovers in the first half, leading to dangerous moments and we were a little wasteful. Start to the game excellent, got them on the back foot, scored early from a set piece and then we should have been two or three going in at half-time with some of the openings we had."
The head coach added: "I thought we dealt with going back to 1-1 very well. Made a substitute, reset and then kicked on which is brilliant mentality from the team."
Tolaj came up with a superb first-time finish to put Argyle 2-1 up in the 68th minute and Pepple, on as a second half substitute as he made his comeback from a calf injury, added a third goal soon afterwards after some excellent build-up play.
Cleverley said: "When you have got strikers who can turn draws into wins it's a real big asset, and with that moment of magic (from Tolaj) you can see we have got that.
"Then the third goal really impressed me because it's what we addressed at half-time about being a little bit more calm and clinical. It was a great team goal."
Argyle made a strong start against an injury-hit Wimbledon and Mitchell, the loan signing from Charlton Athletic, gave them the lead when he scored at the far post after a corner was fired in by Ronan Curtis.
Cleverley said about Mitchell: "He has been colossal for us since he has been at the club. He's someone that does what you need to do in this league, which is be better than the opposition in both boxes.
"Only Lincoln have been better than us at set plays for this year, which they seem to be pretty much one better than us in everything we do in the second part of the season! Really pleased with Mitchell, popping up with another important goal to cap off a really fast start."
After conceding the Wimbledon equaliser, Cleverley was understandably delighted with the response of his players and the way they reasserted their authority on the match.
Cleverley said: "I have got a real trust in our players being able to create (chances) at the minute. I think 23 shots away from home, nine on target, and that has pretty much been every game.
"Last week (in the 2-2 Devon derby draw against Exeter City at Home Park) we were nowhere near it with the ball and we still had 10 shots on target, so 19 shots on target in two games, I will always feel like we will create a moment to score again.
"What we had to do was make sure we were tighter. I thought we were a little bit too open first 20 minutes second half. The key to the whole thing is the mentality of the players, the belief of the players, the togetherness of the players to come back from a setback is gold dust."
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