Saints were issued with two 3-0 defeats and a suspended £40,000 ($71,300) fine by the SPFL after being found to have breached COVID-19 protocols when an outbreak forced the cancellation of games against Hamilton and Motherwell in October.
Killie was also handed a walkover defeat and a suspended £40,000 fine when it had its own clash with Motherwell postponed the same month.
However, both clubs insisted those punishments were overly harsh and took their appeal to the Scottish Football Association, which has quashed the forfeits and handed out £20,000 ($35,700) fines, £10,000 ($17,900) of which are suspended.
St Mirren stated the reversal of the punishment was a "victory for common sense".
"The decision of the Appeal hearing that the matches be rearranged is a victory for common sense and the reduction of the fine from £40,000 suspended to £20,000 with £10,000 suspended is acknowledged by the Club," a statement from the club read.
"We hope that as we progress through this difficult time, no other Club faces the trials and tribulations that St Mirren and Kilmarnock have gone through and instead a common sense and supportive approach is taken by governing bodies to support members in unprecedented times."
All three fixtures will now be rescheduled.
The ruling is the latest embarrassment for the SPFL, which has been criticised for its role in Celtic's controversial mid-season trip to Dubai for a training camp.
Despite Hibernian's protestations, the league moved Celtic's fixture with the Edinburgh club from last weekend to Tuesday (AEDT) to allow the Scottish champion extra time in the Middle East.
On its return to Glasgow, Celtic defender Christopher Jullien tested positive for coronavirus, forcing 13 other players into self-isolation for Tuesday's (AEDT) 1-1 draw.