And Sydney will be without Justin McInerney for three matches after the midfielder was cited for a bump on Brisbane's Brandon Starcevich.
In the fourth quarter of Saturday night's game, won 17.11 (113) to 14.13 (97) by the Bulldogs, Cleary was moving down low to pick up the ball, with Jacob Konstanty attempting to tackle him from behind.
Archer, 22, flung himself forward to attack the contest and went over Cleary from the front, collecting him in the head with his knee.
Cleary, 23, was knocked out and play was stopped as he received medical attention before being taken off on a stretcher.
He was later taken to hospital as a precaution and while he will enter concussion protocols, Cleary has avoided any serious structural injury.
When asked if he expected the match review officer to look at the collision, Bulldogs coach Luke Beveridge said: "I wouldn't have thought so."
But the incident was considered careless conduct, severe impact and high contact, drawing a three-game suspension.
Unless the Kangaroos successfully challenge the ban, Archer, son of club great Glenn Archer, will miss games against Melbourne, Adelaide and Sydney.
McInerney is set to be out for matches against Fremantle, North Melbourne and Collingwood for his bump on Starcevich in Sydney's loss to Brisbane.
Starcevich was concussed and the incident was ruled as severe impact, high contact and careless conduct.
Bulldogs coach Beveridge was leaving the coaches' box for the final siren when the Archer-Cleary incident occurred.
"From the box, it almost looked like, remember, we used to watch Happy Days ... you can't make light of this, but you remember the Malachi brothers, the 'Malachi Crunch'?" Beveridge said.
"From where I was, it just looked like just a bad crash, and players went hard and Luke's come off second best."
The 'Malachi Crunch' involved two demolition derby cars crashing into an opponent simultaneously.
North Melbourne coach Alastair Clarkson had described the incident as "an unfortunate collision".
He was uncertain how the MRO would assess the case, but noted it was their duty to look at collisions that forced players from the field.
When asked if there was anything Archer could have done to mitigate the contact, Clarkson said: "I don't really know the answer to that.
"They're both young players just trying to make their way in the game. So there's no malice in it whatsoever.
"One is coming in hard to compete and the other guy's going in low.
"If you decide to go in low, it better not be that you take the legs of the opposition.
"If you stay upright though, in terms of Arch coming in, then you run the risk of someone low and hitting them in the head, with your legs or whatever."
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