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.
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 precious giving David Walsh no chance of stopping it.
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.
Chris Shields and Joe Thomson were also shown red by referee Tim Marshall late in extra-time.
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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