First-half goals from Mathias Doumbe and Charlie MacDonald, plus substitute Jabo Ibehre's cool late finish, condemned the Grecians to their fifth straight defeat on the road.
The Dons dominated from the start and Dean Bowditch signalled their intent when his low snap-shot was superbly tipped around the post by Exeter goalkeeper Artur Krysiak after only 35 seconds.
But the home side needed a big slice of fortune to take the lead in the 17th minute when Doumbe's 25-yard shot took a wicked deflection off Exeter debutant Jonathan Fortune and looped past Krysiak.
MacDonald netted his first goal in 11 games to double the Dons' lead 10 minutes later, nipping in ahead of defender Troy Archibald-Henville to smartly turn in Alan Smith's low cross.
Exeter improved after the break and Jamie Cureton curled a good chance straight at David Martin, who then produced good saves to keep out substitute Chris Shephard's snap-shot and John O'Flynn's header, but Ibehre sealed the win 12 minutes from the end when he raced clear to poke the ball past Krysiak one-on-one.