But Flannery took a full part in the Captain's Run session this morning at the RDS and is fit to start tomorrow's eagerly-awaited clash with the Wallabies at Croke Park (kick-off 3pm).
As per the team announcement on Wednesday, the uncapped Sean Cronin will provide the hooker cover on the replacements bench.
Ireland coach Declan Kidney said: "Jerry's good, he trained away this morning. It's unfortunate that John (Fogarty) lost out last night, but that's the nature of it - you have to look after tomorrow's team first.
"The lads who played for Ireland 'A' last night, Denis (Fogarty) and Andy Kyriacou, went very well. So, Jerry will start and Sean will be on the bench."
Focusing on Sunday's opponents, Kidney holds Australia in high regard and he praised Robbie Deans' men for their game-changing abilities.
"They are a clever team tactically and you could have four or five different approaches coming at you," he said.
"Like all Tri Nations teams, they have learned off one another. They have the tactical nuances to change a game at any stage."
With memories of last season's Grand Slam success still fresh, Kidney is mindful of the increased expectations as his players prepare to take on Australia and South Africa, two of the world's top three sides.
"People need to be realistic in their expectations and I think that's what we want to be with ours," he added.
"The important thing is to try and get ourselves going, know what worked for us last year and build from there."