After the incident was reviewed by the match referee Jeff Crowe, Lyon was charged with conduct contrary to the spirit of cricket, a level one offence.
He was found to have breached Article 2.1.1 of the ICC Code of Conduct for Players and Player Support Personnel, which relates to "conduct that is contrary to the spirit of the game".
In addition, Lyon has had one demerit point added to his disciplinary record, a first offence for the player since the introduction of the revised Code in September 2016. If a player accrues four demerit points within 24 months, he receives a one-Test or two-limited-over game ban.
Lyon is believed to have contacted de Villiers overnight to apologise. He had also accepted the charge and no hearing was required.
The ICC decided, however, that no action would be taken following a confrontation between David Warner and Quinton de Kock during the tea break on day four.
Adam Gilchrist, the former Australian wicketkeeper and captain, said the team would need to reassess how they reacted to such incidents.
"As an outside observer, I think you would find that a little bit off-putting at times, a little bit bad taste at times," Gilchrist told SEN Radio. "And the question may even come over all those eras as a general statement. Australian teams have generally been at the top of the pile, not every minute of those times, but generally they're a very competitive, world class team,and some would say they don't need to do that.
"Why do you need to present that somewhat ugly look if you're playing such good cricket? And they're not good images and it's hard to know, to comment specificially about this incident overnight, and any other time, unless you're there and know the ins and outs of what was said and what sparked it and the verbal volleys that would have been thrown around.
"Very hard to comment on the detail of it but no denying that some of the parts of the celebration of the run-out of de Villiers and then obviously this incident that I'm sure you're getting to, of this leaked dressing room footage, it's not a very good look. I think it needs to be considered how to react in certain scenarios and learn from the scenarios."
Speaking about Warner, Gilchrist said the Australian vice-captain was not projecting the image of a leader. "I think with Davey...there is no one denying his capabilities with the bat in hand. It's funny...he came into cricket and had his natural aggression mindset both with bat in hand and in the field," Gilchrist said. "He used to pride himself being the guy that got into the verbal stoushes and was a leader of the aggressive mindset. But he then went the other way and he was very, very outright in saying 'I've put that away, that's not me any more'.
"It was really extreme the opposite way, and now he's come back again saying 'old Davey's back' and all his team-mates are saying 'the Reverend's gone, Bull's back'. It's always a worry in any situation when someone is so extreme on one direction or the other. I think Davey's got to find somewhere in between that. He does pride himself in being a leader of the team, he did that very well in the T20s [against New Zealand and England recently] as captain but what we've seen in the last 24 hours probably isn't the images that you want your captain projecting."