Midfielders Black and Santana were fined two weeks' wages after being shown the equivalent of red cards, while defender Jonsson was docked one week's pay for being yellow carded.
It is understood former manager Csaba Laszlo failed to adhere to SPL rules when it comes to internal discipline, forcing the club to scrap the fines rather than lose an appeal made by the players on a technicality.
The decision reportedly saved Santana and Black around £4,000 each and Jonsson £3,000.
The news emerged on the day Hearts were due to face Hamilton for the first time since December's controversial clash, which also saw Accies striker Leon Knight, Jambos masseur Alan Robson, defender Ismael Bouzid and captain Michael Stewart red carded, although the latter had his reduced to yellow on appeal.
New Hearts boss Jim Jefferies, who dramatically returned to the club two hours after Laszlo was sacked at the end of last month, spoke in the build up to today's game of his desire to establish a stricter code of conduct at Tynecastle.
Jefferies insisted this morning it was his decision not to allow Santana, Black and Jonsson's cases to go to appeal in a bid to wipe the slate clean before tough new disciplinary measures kick in.
He told the club's official website, www.heartsfc.co.uk: "I came into the club in the middle of the situation, and decided with support from the club that we should draw a line under what happened and start afresh.
"While it's a clean slate for everyone, I've told the players that anything in the future will of course be dealt with."
PFA Scotland chief executive Fraser Wishart told the Sunday Herald: "Through our efforts, players are becoming more aware that they have the same rights as any employee under employment law.
"PFA Scotland will continue to ensure that our members are given their entitlement to due process, confidentiality and appeal if required.
"Clubs cannot simply impose discipline upon players without adhering to the law."
Source: Team Talk