The victory means that departing Linfield boss David Jeffrey has won 31 trophies with the Blues, matching Roy Coyle's record during his reign.
Andy Waterworth, Aaron Burns, Michael Carvill and Billy Joe Burns scored their spot kicks while only Gary McCutcheon found the net for the Crues.
Speaking to UTV after lifting the title, David Jeffrey said: "The focus all week has been on them performing well so that the club would be successful and as always with the club success, you do get that personal success and it would be churlish to say that isn't satisfying.
"The most satisfying thing is when you have a group of men you've nurtured and looked after and you see them developing.
"This team are developing and part of that education is winning trophies and this has been a good learning curve for them."
Crusaders almost took the lead on four minutes, a goalbound header from Joshua Robinson was cleared off the line by the alert Ivan Sproule.
The Crues certainly posed the most threat in the early stages forcing Jonathan Tuffey to push away a powerful header from Jordon Owens on eight minutes.
Sproule used his pace to create a good break for the Blues on 17 minutes, but his cross was cleared by the Crues defence.
That was to be Sproule's final contribution as he hobbled off on 30 minutes with Aaron Burns coming off the bench.
The Blues had managed to stem the Crues attack but they were struggling to create any real efforts on goal.
I’ll go home and I’ll be very thankful then I’ll look forward to going to my work tomorrow.
Eventually they did manage to test O'Neill with first Philip Lowry connecting with a snapshot which the keeper got behind and in the next attack a crisp shot on the turn by Andy Waterworth was straight at the Crues keeper.
In first half stoppage time Linfield broke out of defence with Jamie Mulgrew spreading the ball wide to Tipton who cut inside and fired across to Waterworth whose run was brought to a halt by Leeman.
From the free, Niall Quinn's drive hit a ruck of players and was hacked away before a Linfield player could force a shot on goal.
The Blues were quick off the blocks after the restart with Aaron Burns slipping the ball to Tipton who clipped a shot just over the bar from a few yards out.
A great run and cross from Billy Joe Burns was well cut out by O'Neill, but it was Burns again with the next chance this time a sweet half volley that skimmed the bar.
Linfield were beginning to get on top with the Crues now relying on a quick break.
The best chance of the game came on 68 minutes when a long throw by Burns missed a cluster of players and fell to Tipton in front of goal but the Linfield striker failed to connect.
With ten minutes to go, Mark McAllister came on for Tipton and made an instant impact with a superb run down the right flank and he delivered an inch perfect cross for the unmarked Aaron Burns but his header flew inches wide of the far post.
Another superb move by Linfield carved out a great chance in the last minute of normal time with Billy Joe Burns linking up with Gault who crossed for McAllister who drove the ball towards goal but his effort was blocked and cleared.
It was end to end in extra time with both teams having chances to win it. Aaron Burns fired just wide while for the Crues Chris Morrow brought a superb save out of Tuffey.
Crusaders: O'Neill, King, Smith, Leeman, Magowan, Owens, Heatley, Snoddy, Caddell, Hanley, Robinson. Subs: McAllister, Morrow, McMaster, McCutcheon, McAllister.
Linfield: Tuffey, Gault, Haughey, Waterworth, Lowry, Burns, Ward, Tipton, Mulgrew, Sproule, Quinn. Subs: McVey, Carvill, Burns, McAllister, Deane.
Referee: Hugh Carvill.