McCarthy has been fined R50 000 (R25 000 suspended) for comments he made towards referee Phillip Tinyani, with City receiving the same sanction for misconduct.
Meanwhile, Mbombela were fined R50 000 and docked three points for fielding the suspended Mxolisi Mayongo in an NFD clash with Tshakhuma Tsha Madzivhandila on November 18.
United won the game 3-0 at Kanyamazane Stadium.
Mayongo has also been hit with a four-match ban in addition to the automatic one-match suspension he earned by picking up four yellow cards.
The PSL released a statement, which reads: 'The following matters appeared before the Premier Soccer League Disciplinary Committee this week.
'Below is the summary.
'1. ROYAL EAGLES FC:
The Club was charged with failing to submit their Security Operational Plan to the Premier Soccer League at least five days before their match against University of Pretoria FC as stipulated in the NSL Security Manual. Royal Eagles was fined R 40 000.00 of which R 20 000.00 was suspended for a period of 12 months and were ordered to pay a proportional share of the costs of the sitting.
'2. CAPE TOWN CITY FC and BENNI MCCARTHY:
Mr. Benni McCarthy and Cape Town City were charged by the PSL Disciplinary Committee with misconducts following comments made by Mr McCarthy towards match official, Mr Phillip Tinyani. Mr McCarthy and Cape Town City pleaded guilty to the charge. They were each fined R 50 000.00 of which R 25 000, 00 was suspended until the end of the 2018/19 season.
'3. MBOMBELA UNITED FC and MXOLISI MAYONGO:
The Disciplinary Committee endorsed the plea agreement between the League and Mr Mayonga and Mbombela United arising from an incident when Mr Mayongo participated in a match against Tshakumatsha Madzivhadila FC whilst under suspension. The Member Club was sentenced to a deduction of three match points during the current 2017/2018 NFD season and a fine in the amount of R 50 000.00 of which R25 000.00 was suspended for a period of 24 months. Mr Mayongo was sentenced to a four-match suspension in addition to the automatic one-match suspension earned by reason of his four cautions in the NFD League Competition. Of these four matches, two matches were suspended for a period of 24 months from the date of endorsement of this plea agreement.'