Preston secured their sixth away win of the season to pile more pressure on relegation-threatened Exeter.
Preston dominated the first half but only had one goal to show for it, Danny Mayor's right-wing cross was turned in at the back post by Iain Hume.
Exeter equalised when Elliott Frear laid the ball off to Liam Sercombe to fire home from the corner of the box.
Hume scored his second when he rounded goalkeeper Artur Krysiak, who had failed to deal with a long goal-kick.
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Exeter City manager Paul Tisdale told BBC Radio Devon:
"I thought we were going to get the winner.
"I'm certainly not going to tell anybody any criticisms of my players, we've got nine games to go and I don't think that's going to help.
"The difference between the two sides was their striker, Iain Hume.
"We had lots of endeavour and I've got no gripes at all with the way we applied ourselves."