The Dagestani then landed a number of powerful shots on the ground before eventually executing the submission in the fourth and McGregor is banned from contact training until October 28.
It is common practice for the UFC to hand out medical suspensions and McGregor would not have fought again within the next month anyway.
But the damage was not just physical for the defeated lightweight and he could yet be handed a longer suspension by the UFC and also Nevada State Athletic Commission for his role in the ugly brawl that followed the climax to the fight.
Khabib jumped over the cage to attack McGregor's team-mate Dillon Danis after being gestured to come outside, sparking a chaotic melee.
One of the Dagestani's team, his cousin, was then seen entering the octagon and McGregor landed a seemingly unprovoked punch on him, prompting two more of the entourage to come in and attack the 'Notorious'.
Zubaira Tukhugov, a former UFC fighter himself, was the guilty party, catching the 30-year-old from behind after scrambling over the cage.
On the face of it, Khabib triggered the brawl but McGregor's punch on the champion's cousin escalated matters and could see him given a lengthy suspension from competition.
His opponent is likely to be given a more serious punishment from the Nevada State Athletic Commission who also withheld his £1.2million purse after reviewing the footage.
In the immediate aftermath McGregor was not judged to have been culpable for the frenzy and was allowed to take home his £2.3 million.
The NSAC and UFC can both impose separate sanctions on the fighters as the contest in Las Vegas was authorised by the local authority.
UFC president Dana White questioned whether Khabib might have his visa revoked in his first press conference after the extraordinary brawl but has since softened his prediction.
He believes a percentage of the Russian's winnings and short suspension would suffice although he admitted they may take all of his purse away.
The veteran promoter said: 'I think they should take £250,000 from him. (He) absolutely keeps his title. And he's going to get suspended, so maybe you give him a four to six months suspension.
'They took his whole purse right now and they're talking about keeping his purse,' the UFC chief said on TMZ Live.
'You should not be able to keep his whole purse.'
McGregor's fierce rivalry with Khabib was exacerbated by the months of trash-talking leading up to their fight.
The Irishman offered the devout Sunni Muslim whiskey at a press conference in New York and also called him a 'Dagestani rat'.
McGregor branded Khabib's manager Ali Abdelaziz a 'terrorist', 'snitch' and 'rat', antagonism that the Dagestani admitted drove him to kick off the brawl.
The biggest fight in UFC history was marred by ugly scenes that threatened to turn into a full-scale riot and now both pugilists must await further punishment.
