The big call for John Hughes came with the recall of Richie Foran and Josh Meekings to the starting line-up at the expense of Danny Williams and Liam Polworth. Jordan Roberts and Greg Tansey were also out, with Gary Warren and Carl Tremarco returning from suspension.
Hibernian made one change from the team that lost the League Cup Final against Ross County, with Kevin Thomson dropped in favour of James Keatings.
Despite Stokes and Jason Cummings struggling to gel, Stubbs persisted with the pair.
Foran's start was the most surprising, given that it was his first one since March 2014.
Lewis Horner and Stokes exchanged chances for either side, with both keen to put disappointing weekend results behind them.
However, it was Stokes that would get the second chance, making the most of Carl Tremarco and Danny Devine missing Keatings' cross to finish well after 36 minutes.
Not content with shooting themselves in the foot once, Caley Thistle did it again five minutes later.
Devine gave the ball away to Liam Henderson, he squared for Cummings and when his shot was well saved, Stokes was on hand to slam in the rebound.
Inverness were going down meekly at this stage and should have given themselves a route back into the game at the start of the second half through Tremarco.
Meekings' cross from the right was flicked on by Vigurs and the defender could only turn it over from three yards at the back post.
Hughes threw on Miles Storey and Williams, but bizarrely out of position on the left and right flanks respectively.
It provided little attacking threat as first Stokes and John McGinn were thwarted by Owain Fon Williams at the opposite end.
Meekings and Hughes both lashed volleys wide as Inverness looked desperate, but when Vigurs hammered in his 77th-minute chance, they had some hope.
Mark Oxley's knock and eventual substitution, after numerous accusations of time-wasting, gave Inverness seven additional minutes to save their crown, but time ran out on the cup holders.