The Sky Blues have been promoted back to SkyBet League One after a stunning 3-1 win over Exeter at Wembley.
Willis gave the Sky Blues the lead just after the break with a stunning right-footed curler from 25-yards.
Minutes later Shipley doubled City's lead thanks to the help of a deflection, before Jack Grimmer picked-out the top corner to seal the win.
The victory means Mark Robins' side have been promoted back the SkyBet League One at the first time of asking.
The opening five minutes were as cagey as expected. Marc McNulty's long-range effort send goalwards after a neat Max Biamou knock-down was the pick of the early action but that sailed high over the bar.
A poignant moment followed as the Sky Blue Army, along with the Exeter City supporters, stood as one to applaud on the ninth minute in memory of the late, great, Cyrille Regis before singing the City legend's name.
On the field, Mark Robins' side were having all the chances - First, Michael Doyle's precision ball off the top set McNulty away in the area, but the 25-year-old would have wished for a little less height on the ball from his captain as he struggled to take the pass into his stride and was tackled.
Next, it was McNulty again, who after a stunning 40-pass move played a delightful one-two on the edge of the area before seeing his curling effort saves.
Jordan Shipley cemented his place as a first-team regular this season and has his first sight of goal after 20 minutes but he too was forced to watch his deflected effort sail agonisingly wide.
City came out into the Wembley sunshine after the interval just as strong as they started the afternoon, and took the lead through Coventry born Willis. The defender, up for a corner, hang around for just about long enough on the edge of the area to turn his man and curl a beauty into the far corner. It was a stunner and Wembley erupted with blue.
If you thought the roar for the first would be impossible to top them you would be proven wrong moments later. McNulty raced into the Exeter half before finding Shipley in space who fired over Pym and into the far corner. Just like last year, it was our own academy graduates firing the Sky Blues to silverware.
Robins' boys were running riot. Next it was Liam Kelly's turn. The midfielder charge upfield and skipped his challenge but his low strike skimmed wide.
With twenty minutes to go City sealed it. Grimmer only scores in big games and made sure today was no exception when he found the far corner with his left foot from the corner of the area. It was turning out to be a Sky Blue day in North London.
Despite the domination it wasn't an easy afternoon for Lee Burge who pulled off a stunning save from Jordan Tillson to protect City's lead diving down to his left.
Tom Bayliss made it four at Meadow Lane last week and came close to making it four at Wembley. The teenager twisted and turned his way into the area before forcing a stellar reflex save from Pym.
Exeter did pull one back in the final second through Kyle Edwards but it would only be a consolation.
The Sky Blues are promoted back to League One. Play Up Sky Blues!
Goals: Willis (48'), Shipley (55'), Grimmer (68').
Attendance: 50,196.
Coventry XI: Burge (GK); Grimmer, Hyam, Willis, Stokes; Bayliss, Doyle (C), Kelly, Shipley (Reid); Biamou (Clarke-Harris), McNulty (Ponticelli).
Subs: O'Brien (GK), McDonald, Thompson, Maguire-Drew, Ponticelli.
Exeter City XI: Pym (GK); Sweeney, Woodman (James), Tilson, Harley, Stockley, Moore-Taylor (C), Moxey (Jay), Taylor, Storey, Boateng (Edwards).
Subs: Jones (GK), Archibald-Henville, Simpson, Wilson.