The first half was far from a classic, with neither side having a clear-cut chance of note.
The closest either side came to breaking the deadlock was when Ben Hall rose highest to meet a Cooper corner and saw his effort strike the top of the crossbar.
But eight minutes into the second half, the deadlock was broken. A defensive mix-up from the Blues allowed Jenkins to nip in and strike from just inside the box, finding the bottom corner with a precise shot which gave keeper David Walsh no chance.
Linfield then levelled as McKee met Ethan McGee’s long throw-in with his head, finding a way past Daniel Gyollai at the near post to find the equaliser.
Cooper was shown a red card in the first half of extra-time for kicking out at Russell, leaving his side with a huge ask with 10 men.
It took a moment of brilliance from substitute Thorndike to seal Glentoran’s spot in the quarter-final as his long-range strike with his left foot won it for Declan Devine’s side.
Shields and Thomson were also shown red by referee Tim Marshall late in extra-time.
Former Dundalk player Shields was dismissed for a cynical foul on Dylan Connolly, whilst Thomson was shown his marching orders after provoking a scuffle with the Blues captain, which continued down the tunnel.
Glentoran will discover their quarter-final opponents on Saturday evening with the draw taking place live on BBC Sportsound after the seven other Irish Cup fixtures.
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