According to the ICC website, Lyon 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."
One demerit point has been added to the disciplinary record of the Australian off-spinner, for whom it was the first offence.
The incident occurred in the 12th over of South Africa's second innings on Sunday, following the run out-dismissal of Proteas batsman AB de Villiers.
Lyon dropped the ball, hitting De Villiers on the chest as he lay on the ground after diving in an attempt to make it to the crease at the bowler's end.
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Lyon admitted the offence and accepted the sanction proposed by Jeff Crowe of the Elite Panel of ICC Match Referees and, as such, there was no need for a formal hearing.
The charges were levelled by on-field umpires Kumar Dharmasena and Sundaram Ravi, third umpire Chris Gaffaney and fourth umpire Allahudiean Palekar.
Level 1 breaches carry a minimum penalty of an official reprimand, a maximum penalty of 50 percent of a player's match fee, and one or two demerit points.