The world governing body also agreed to pay 2.5million Swiss francs (£1.64m) in compensation - but only on the condition that criminal proceedings against Havelange and executive committee member Ricardo Teixeira were dropped.
The publication of the report by the prosecutor's office of the Swiss canton of Zug suggests that current FIFA president Sepp Blatter would have been aware of at least one bribe paid to Havelange.
FIFA have published the report on their website, but it leaves big question marks about why no action was ever taken against Havelange or Teixeira, and why the organisation went to such lengths to protect the two senior figures.
The report states: "The finding that FIFA had knowledge of the bribery payments to persons within its organs is not questioned.
"This is firstly because various members of the executive committee had received money, and furthermore, among other things, it was confirmed by the former chief financial officer of FIFA as a witness that a certain payment made to Joao Havelange... amounting to CHF1m was mistakenly directly transferred to a FIFA account; not only the CFO had knowledge of this, but also, among others, P1 would also have known about it."
The person referred to in the report as P1 is not identified, but it also states that P1 and Havelange had signed the marketing agreement with ISL on behalf of FIFA in 1997. It is known that the agreement was signed by Havelange, who was president, and Blatter who was then general secretary.
The documents state Havelange was paid at least CHF1.5m (£1m), Teixeira at least CHF12.74m (£8.37m) and the pair may have received as much as CHF21.9m (£14.4m).
The two men have dominated Brazilian football between them for the last 50 years. Teixeira at one time was Havelange's son-in-law and only stepped down earlier this year from FIFA's executive committee and as head of Brazil's 2014 World Cup organising committee after it became apparent the report would be published.
Teixeira and Havelange also tried to block the publication by going to the Swiss federal court but failed to do so.
Both men have paid compensation, Teixeira of CHF2.5m and Havelange of CHF0.5m, and FIFA who were being investigated for "disloyal management" also agreed to pay CHF2.5m.
The report states: "FIFA declared that it agreed to the conditions; however, in its letter dated January 8, 2010, it made its consent conditional upon the discontinuance of the proceedings against Ricardo Terra Teixeira and Joao Havelange."
The report does confirm that Blatter was not among those on the list of people who were paid bribes by ISL.
A FIFA statement said: "This decision by the Federal Court is in line with what FIFA and the FIFA president have been advocating since 2011, when world football's governing body announced its commitment to the publication of the ISL non-prosecution order.
"This announcement was part of a process of reforms launched at the FIFA Congress in June 2011, the roadmap for which was approved by the FIFA executive committee on 21 October 2011.
"The decision of the Swiss Federal Court also confirms that only two foreign officials will be named as part of the process and that, as previously communicated by the Prosecutor of Zug in June 2010, the FIFA president is not involved in the case ("no Swiss person involved").
Havelange, who is now 96, is still honorary FIFA president, a title conferred on him after he stepped down in 1998 after 24 years as the most powerful man in world football.
He resigned as a member of the International Olympic Committee in December after 48 years on the grounds of ill health, just days before the body was due to sanction him following their ethics committee's own investigation into ISL payments.
Another FIFA executive committee member Nicolas Leoz from Paraguay was previously named in court as having been paid £83,000 by ISL but he was not named in the court report.