Motherwell have been awarded 3-0 wins over both sides and Hamilton have been handed a 3-0 victory over St Mirren after positive Covid-19 tests caused games to be postponed.
The two clubs have also been hit with a £40,000 fine, suspended until June 30, 2020, pending any other breaches of protocol.
A Scottish Professional Football League statement declared that Kilmarnock's breaches included a failure of physical distancing on a coach and during a pre-match meal.
St Mirren admitted the same breaches plus "failing to provide suitable facilities to enable players to observe physical distancing at training and also accepted that players had been car sharing to and from training".
The Paisley club said in a statement: “St Mirren Football Club is disappointed with the outcome of the SPFL disciplinary hearing into the circumstances surrounding our postponed fixtures against Motherwell and Hamilton.
“The hearing found St Mirren guilty of breaching protocols and subsequently imposed 3-0 wins to both Motherwell and Hamilton alongside a £40,000 fine, suspended until June 2021
“The club operated honestly throughout the whole process and will review its position before issuing a further response.”
Kilmarnock themselves added: “Kilmarnock Football Club is bitterly disappointed with the outcome of the SPFL disciplinary hearing into the circumstances surrounding the postponement of our match with Motherwell.
“Following the hearing, Motherwell have been awarded a 3-0 victory while we have been hit with a £40,000 fine, suspended until June 2021.
“The club is currently discussing our position with our legal representatives and will make further comment in due course.”
The decision has had a major impact on the Scottish Premiership table. Motherwell have jumped from eighth place into fifth, and can go to within two points of the top four if they defeat Hibs this Saturday. Dundee United have dropped out of the European places as Kilmarnock drop out of the top six.
At the bottom, meanwhile, Hamilton Accies have moved level with St Mirren on 11 points, though remain bottom due to their inferior goal difference.