Kevin Lisbie converted twice from the penalty spot to help Leyton Orient to their first win in four games.
Orient could not make their possession count in the first half and after the break Lisbie put them ahead when Troy Archibald-Henville handled in the area.
The O's striker had a hand in the second when he set up Jonathan Tehoue's close-range header after Archibald-Henville missed a clearance.
Lisbie added his third when Archibald-Henville tripped George Porter.
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Leyton Orient manager Russell Slade told BBC London 94.9:
"In terms of the league, it was a big win that gets us back on track.
"I wanted a reaction and I got the perfect response today.
"In the end we got the breakthrough we thoroughly deserved."
Exeter City manager Paul Tisdale told BBC Radio Devon:
"The players are all complaining about the first penalty.
"But then we got very spread out. We had no real flow, we didn't find our lines, our pattern or our purpose.
"The scoreline probably tells everything and they were worthy winners, I think."