The hosts scored the only goal after seven minutes when a poor clearance by goalkeeper Lee Burge fell to Harley 25 yards out and his lobbed effort went in off the upright.
Coventry responded with a Jack Grimmer shot that was easy for Christy Pym, while Exeter striker Jayden Stockley was just off target with a fine shot from distance.
Harley saw another goalbound effort blocked and as Coventry countered, Pym stood up well to beat away Marc McNulty’s effort.
Coventry’s best chance fell to Maxime Biamou, who was played in on goal, but Pym again stood up and saved well to preserve Exeter’s lead.
McNulty almost capitalised on a Troy Archibald-Henville error, but was denied by Pym, before the striker saw another effort deflect over the bar.
Substitute Jordan Ponticelli clipped the top of the crossbar in stoppage time for Coventry, but the Sky Blues could not force an equaliser and are now eighth, one point below their opponents.
Colchester will hand late fitness tests to Ryan Jackson and Brandon Comley prior to their clash with Yeovil.
Arsenal secured their place in the quarter-finals of the Europa League following their 3-1 defeat of AC Milan at the Emirates Stadium on Thursday.
Danny Welbeck scored twice against AC Milan to toast his England recall by sending Arsenal into the last eight of the Europa League.
Ipswich striker Joe Garner will not play again this season after it emerged he suffered a fractured skull against Sheffield United last week.