A third arrived from Jack Grimmer with just over 20 minutes remaining to effectively seal the Sky Blues' place back in the third tier of England football, with Exeter only managing a late Kyle Edwards consolation in reply.
The victory hands Coventry their first promotion from any division since 1967, but for Exeter it is playoff heartbreak for the second year in a row.
The defeat will also raise more questions over the future of Exeter boss Paul Tisdale, who is now expected to end his 12-year reign at the club with MK Dons thought to be interested in appointing him as their new manager.
It was no surprise that the first shot of the afternoon came from Coventry top scorer Marc McNulty, who collected Maxime Biamou's knockdown before firing an ambitious dipping volley over the crossbar from 25 yards.
McNulty had a clearer sight of goal 10 minutes later when he was played through, but he was unable to get the ball under his control and that allowed Jordan Storey to get back and make a crucial last-ditch challenge inside his own area.
Coventry were slowly beginning to gain control of the match, and McNulty continued to look the most likely to open the scoring, drawing a first save from Christy Pym with a low strike from range which came at the end of slick passing move.
Exeter looked to produce their own string of passes moments later, but they only succeeded in giving the ball away in a dangerous position and that allowed Shipley to fire a deflected effort wide of the target.
A head injury suffered by Chris Stokes slowed Coventry's growing momentum, with the Sky Blues being forced to play with 10 men while he was getting patched up, allowing Exeter to work their way back into the match following a period on the back foot.
Coventry responded with a powerful Shipley strike which stung the palms of Pym before McNulty sliced another sight of goal off target from the edge of the box, but the first half came to an end with both sides having struggled to provide a moment of telling quality.
It was an entirely different story in the opening stages of the second half, though, with Coventry immediately getting on the front foot and McNulty drawing an early stop from Pym with a curling effort that needed to be pushed behind at the near post.
It was the more unlikely source of Willis who provided the breakthrough, and he did it in some style while still up from the resulting corner, collecting the ball with a fine first touch before bending a stunning finish into the far corner from just outside the area.
If the opener was all about a moment of quality which had been sorely lacking up to that point, the second was all about luck when it arrived just six minutes later, with Shipley bursting on to McNulty's pass before seeing his shot deflect off a defender and loop over the keeper into the top corner.
Suddenly Exeter found themselves needing to throw caution to the wind as they faced the prospect of playoff heartbreak for the second year in a row, although that left them susceptible to the counter-attack and Shipley almost capitalised on that with a long-range strike which needed to be tipped past the post on the hour mark.
A third goal did arrive just eight minutes later as Coventry put the game to bed, and Grimmer provided the pick of the bunch with a curling effort into the top corner after being teed up by McNulty once again.
Exeter refused to give up hope despite their three-goal deficit, and they almost gave themselves the platform for a comeback just four minutes later when Lloyd James latched on to a cross at the back post and nodded his effort across goal and narrowly wide of the target.
Burge was then finally forced into his first testing save of the afternoon with 15 minutes remaining when Harley looked to pick out the bottom corner from outside the area, seeing his goalbound effort tipped around the post.
Coventry still looked capable of adding to the scoring themselves, though, and it took a fine reaction save from Pym to deny Tom Bayliss a fourth when he danced into the area before seeing a deflected shot almost sneak past the Exeter keeper.
The closing stages saw Exeter desperately push for an unlikely route back into the match, and they came close on a couple of occasions when Matt Jay's powerful strike came off the outside of the post and Storey sent a header looping wide.
However, when the goal finally arrived in the 89th minute it was too little too late, although Edwards will no doubt still treasure the Wembley strike as he capped a bright cameo display by cutting inside and picking out the far bottom corner with aplomb.
Jayden Stockley had a chance to crank up the Coventry nerves in the fourth of five minutes' injury time when he took the ball down inside the box, but when he fired just wide of the target it was clear that there would be no way back for Exeter.
EXETER (4-4-1-1): Pym; Sweeney, Storey, Moore-Taylor, Woodman (James 63'); Taylor, Boateng (Edwards 73'), Tillson, Moxey (Jay 63'); Harley; Stockley
COVENTRY (4-4-2): Burge; Grimmer, Willis, Hyam, Stokes; Bayliss, Kelly, Doyle, Shipley (Reid 73'); McNulty (Ponticelli 82'), Biamou (Clarke-Harris 51')