Onyango, 35, won his seventh league title in South African football last season and is widely considered as the finest shot-stopper on the continent.
The Cranes captain was due to join the squad for their training camp in Dubai but Masandawana informed McKinstry that their call-up had been rejected due to the issue of being quarantined for two weeks after his return.
"We are very disappointed in Mamelodi Sundowns' position regarding not releasing Denis Onyango for international duty during the October 2020 FIFA dates," the FUFA statement read.
"As a national team we have been clear that we would not call players to this camp who would have to quarantine on return to their respective clubs. (Eg. Players based in Isreal and USA)
"We asked Sundowns for evidence of the regulation regarding quarantine, and they were only able to provide information regarding tourists arriving in South Africa, and not residents as is the case for Denis Onyango."
McKinstry added the decision goes against what the player wishes and questioned the professionalism of the 2019/20 domestic treble winners.
"...We would like to state however that Denis Onyango has always been eager to join us in Dubai and we feel he has been put in a very difficult position by his employers," the statement continued.
"As such, we attach no blame in this situation to the player who remains a key part of our plans for AFCON 2022 and World Cup 2022 qualification.
"Mamelodi Sundowns are one of the leading clubs in Africa, and this situation, in our opinion differs greatly from the levels of professionalism we have come to expect from them over the years."