Baldock had been guilty of three glaring first-half misses, heading wide of an unguarded net and twice failing to beat goalkeeper David Martin when through one-on-one.
But Cotterill revealed: "I told Sam that I wouldn't be substituting him no matter what happened in the second half.
"I wanted him to keep getting into scoring positions. He deserves all the credit for turning things around, but hopefully what I said gave him a boost.
"It is not the first time I have told a player I wouldn't substitute him. Sometimes you can be tempted into panic changes when actually your team are doing okay.
"I can't believe we didn't win the game. It should have been 4-2 to us at half-time and instead we went in two goals down. That was a travesty and we continued to create chances throughout the game."
Baldock capitalised on a fortunate ricochet to shoot past Martin on 57 minutes and then forced the ball over the line 14 minutes from time after a corner had been headed into his path.
Dons centre-back Shaun Williams had fired his side ahead after 17 minutes, chesting the ball past City debutant Adam El-Abd and beating Elliott Parish for his 10th goal of the season.
Ben Reeves was then allowed to burst between defenders onto a 36th-minute Samir Carruthers through-ball and coolly chipped over the advancing Parish.