Grecians midfielder Ryan Harley struck a low left-footed shot past Cherries goalkeeper Ryan Pryce after 68 minutes to give the West Country outfit their first three points since dropping into non-league football back in 2003.
In an uneventful first half it was Exeter who, despite having little possession, spurned the best of the chances on offer.
Bournemouth manager Kevin Bond persisted with a one-man attack which failed to really trouble a well-organised Exeter defence, and when the only goal arrived it had an air of inevitability about it.
Rob Edwards broke through the midfield before laying the ball on to Harley, who took one touch to steady himself and a second to beat Pryce in fine fashion.
The hosts finally registered their first shot on target after 75 minutes through Brett Pitman but that was as good as it got for Bond's sorry outfit.