The Candystripes made it through to the final following a 25-minute strike by Rory Hale.
But it was Doherty who kept City in the game pulling off a string of superb faces to deny Rovers an equaliser at The Showgrounds on Monday night.
Said Shiels “He has been a sensational captain. I’m really pleased for him because he put in a top captain’s performance.
Shiels had to parade a young side with Jamie McDonagh, Darren Cole, Gavin Peers and Eoin Toal all missing because of suspension, recent signing Ally Roy cup-tied and Conor McDermott and Nicky Low also unavailable because of injury.
And striker Rory Patterson left the club last week to join north Belfast side Crusaders.
“The players rallied around each other. You could see the young lads were overawed but the experience they get from this will certainly stand them in good stead,” added Shiels.
“It (the win) means so much to me personally and you can see it with the players too.
“They gave a message. The answered that question tonight. You could see the commitment levels, the energy and the work ethic that we didn’t have in the second half on Friday night.”
Lewis Morrison missed two great Sligo chances either side of Hale’s goal as he failed to connect Kris Twardek’s shot before blasting over on 34.
Hale struck Derry’s goal as he lashed to the top corner of the net after Splaine’s ball past John Mahon.
The first of Doherty’s superb saves came before the break as he tipped over Mikey Brennan’s powerful header.
As Sligo produced pressure following the restart, Regan Donelon fired inches over the Derry crossbar although the goalscorer’s brother then had a chance to double the visitors’ lead before being denied by home keeper Mitchell Beeney.
The keepers continued to make fine saves at either end with Doherty pushing away a Raffaele Cretaro effort before Beeney stopped an Aaron McEneff shot moments later.
Doherty’s heroics continued until the end with him grasping another Cretaro chance as Derry held on to set up a chance to increase their record haul of 10 triumphs in the competition.
City now face Cobh Ramblers in the final after their surprise 1-0 win over Dundalk.
The date and time for the final has yet to be formally announced.
Next up for Derry is an away game this Saturday, August 11 in the Irish Daily Mail FAI Cup against Blarney Utd at O’Shea Park, Blarney.
Kick off is at 5 pm.