Unfortunately, Flannery has grown used to being on the sidelines in recent seasons having missed the 2009 Lions tour, last year's summer tour to New Zealand and Australia and the 2011 Six Nations.
But the steadfastly professional manner in which he handled his latest setback has left a mark on everyone in the Ireland camp.
In a nice touch, he was given the honour of presenting the players with their jerseys for Saturday's game in Auckland and spoke movingly of what it means to play for your country and the esteem in which he holds his team-mates.
It was no surprise to see Ireland captain Brian O'Driscoll and Stephen Ferris pay special mention to the popular 32-year-old before he leaves New Zealand.
"It's nice to back up all our talk from during the week. There were some very passionate words said by guys who weren't even in the 22. That's where this performance came from," admitted O'Driscoll, in the aftermath of the 15-6 defeat of Australia.
"There were some poignant moments throughout the week and I don't think a lot of guys will forget Jerry handing out the jerseys at the captain's meeting."
Highlight Flannery's role in spurring the side on to victory, Ferris said: "Jerry has a calf injury and will be leaving us soon. It was quite emotional listening to him. You could see how much it meant to him. I think the lads went out and did it for him."
Ireland's first World Cup win over the Wallabies at the fifth attempt released plenty of emotions for the players, coaches and fans alike.
O'Driscoll, with the side of his face stained with blood from a head wound, savoured that winning feeling on the night of his 115th appearance for Ireland.
"Seeing that happy dressing room again when you know you've really put your body on the line - that's what playing professional rugby is all about for me," he told RTÉ Sport.
"When the day comes that you give that up, that sort of thing is what you'll miss most.
"The contentment knowing that you've put your body on the line for 21 other guys, a 30-man squad and all the management. To see the smiles on all their faces makes playing footie all the better."
Lansdowne Road 2002, Lansdowne Road 2006 and Eden Park 2011. O'Driscoll has been part of three winning Irish teams against Australia and undoubtedly this was the sweetest success of all.
Their recent form suggested Ireland would struggled against the Tri Nations champions, but internally the belief was there that Declan Kidney's men could produce something special.
"Mentally we were in a place where we felt as though we owed ourselves a big performance. Much as we owed the Irish public one, we owed ourselves one first and foremost," added O'Driscoll.
"There was a tension in training and a sense that the performance was coming. It was just a matter of making it happen."
Follow the Ireland team in New Zealand on www.twitter.com/irfurugby.