Karl Robinson's side was sprinkled with youngsters and it was the League One outfit who started the brighter, creating a couple of early openings.
Banton forced Matt Duke into a fingertip save with an excellent curling effort from the edge of the box and moments later he had to be alert to keep out a close-range shot from Patrick Bamford.
But Dons broke the deadlock in the 13th minute when Reeves cut inside before beating Duke with a low drive from the edge of the box via the upright.
Duke kept Cobblers in the game when he denied Shaun Williams with a point-blank save from close range.
Roy O'Donovan's cheeky 25-yard chip left Ian McLoughlin stranded only for the ball to land on top of the net. And just before the break O'Donovan's fierce drive was parried by McLoughlin.
But Duke was soon called into action after the restart, saving well from Bamford after he broke into the box before Dons doubled their lead in the 53rd minute.
Duke turned away a shot from Banton and, from the ensuing corner, saved from Dele Alli but Banton struck home the rebound.
George Baldock should have increased Dons' lead when he headed wide from Reeves' cross.
O'Donovan reduced the arrears in the 77th minute, latching on to a loose ball before finding the bottom corner from 15 yards.
Matt Heath went close to an equaliser when he headed wide at the far post and substitute David Moyo blasted wide late on as Northampton finished with a furry, but it was not be for the hosts.