Doumbe's 58th-minute header and substitute Lowe's cool last-minute finish handed the in-form Dons their third win in four games, leaving Swindon without a win in four.
The Robins were fortunate not to be reduced to 10 men early on in Tuesday night's League One encounter at stadium:mk when goalkeeper Wes Foderingham escaped with just a yellow card for handling outside his box as Dons striker Patrick Bamford closed him down.
Bamford then had a goal-bound shot blocked by Alan Navarro after racing clear onto goalkeeper Ian McLoughlin's long punt and poking the ball past Foderingham.
Swindon held their own in a tight first half and Andy Williams had a goal ruled out for a foul on McLoughlin as he headed in Shaun Williams' mis-cued clearance and drilled another shot into the side-netting.
But Doumbe broke the deadlock 12 minutes after the break when he nodded in Jon Otsemobor's cross from close range.
And Lowe sealed the win at the death when he controlled the ball on his chest and curled a neat finish past Foderingham for his 11th goal of the season.