Kevin Ellison's brace led Morecambe to their first win of the season as they ended Exeter's unbeaten league run.
Morecambe's Jack Sampson had a header cleared off the line, but the unmarked Ellison nodded home just after the break to put his side in front.
Sampson and Ellison combined for the second as the striker lobbed keeper Artur Krysiak from 12 yards out.
Aaron Davies and John O'Flynn both went close for the visitors, but home keeper Barry Roche kept them at bay.
VIEW FROM THE DRESSING ROOM
Exeter manager Paul Tisdale told BBC Radio Devon:
"It was a very competent first half and a poor second half.
"We had three or four really good chances in the first half, but I'm not going to show any frustration to the players - they want to score, but some days they don't go in.
"My main instructions [at half-time] were to be as good as we could in the first five minutes and make sure we got back in control like we were in the first half, but we didn't do that, did we?
"I was disappointed with the first goal. He had a free header from eight or nine yards out, which is very disappointing from a defensive point of view."
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