Conlan and Donnelly have since turned professional and are not impacted by sanctions including an obligation to follow integrity education programmes.
The three boxers did not attempt to manipulate an event at the Rio Games.
The Olympic Council of Ireland and British Olympic Association were also sanctioned with a reprimand.
Participants are are not permitted to bet on Olympic events and the trio violated the Rio 2016 Rules on the Prevention of the Manipulation of Competitions.
London 2012 bronze medallist Conlan, who suffered a controversial bantamweight quarter-final defeat in Rio, placed bets on boxing contests on 8 and 9 August.
Both bets, in his weight division but not on his two bouts, were lost.
Donnelly betted on himself to lose his welterweight fight against Tuvshinbat Byamba on 11 August - the Ballymena man won on points.
His explanation to the IOC was that he had "bet without intending to cheat by losing his match to win his bets, rather, winning the bets would be some compensation in the event he lost his match".
Donnelly lost at the quarter-final stage while middleweight Fowler, who also bet on boxing events, was beaten in his opening bout.
The IOC said the trio must successfully follow the IOC education programme to be eligible for Toyko.
The are also required to support, through active participation, education programmes organised by the either the AIBA, IOC or their Olympic association.
The Olympic Council of Ireland and British Olympic Association were "sanctioned with a reprimand for not having properly informed its athletes about the content of the different rules applicable to them on the occasion of the Olympic Games in Rio, as well as about the content of the contract signed with them".
They are both "requested to make sure that the team preparation for the Olympic Games (winter and summer) includes complete education on the prevention of the manipulation of competitions and betting on the Olympic Games.
Meanwhile. it is recommended that the AIBA put in place "education programmes on the prevention of the manipulation of competitions and betting on the Olympic Games".
Irish pair Michael Conlan and Steven Donnelly have been issued with "severe reprimands" along with Britain's Antony Fowler for betting on Olympic events.