Havelange stood down after being targeted in the findings of an Ethics Committee set up by FIFA to investigate a scandal involving the now bankrupt Swiss-based marketing agency ISL and World Cup television rights.
The Brazilian's conduct was described as "morally and ethically reproachable" in the report into the affair headed by the head of the committee, Hans-Joachim Eckert.
Havelange, now 96 and in poor health, is alleged to have taken improper payments during his time serving as FIFA's seventh president between 1974 and 1998.
His successor, Sepp Blatter, is said to have known about one payment to ISL destined for Havelange of 1.5 million Swiss francs ($1.6 million), with the report concluding that Blatter's conduct was "clumsy" but not "criminal".
Blatter welcomed the report's findings.
"I have taken note of the report from the chairperson of the adjudicatory chamber of the FIFA Ethics Committee, Hans-Joachim Eckert, regarding the examination of the ISL case," Blatter said in a statement.
"I note in particular that, in his conclusions, chairman Eckert states that 'the ISL case is concluded for the Ethics Committee' and that 'no further proceedings related to the ISL matter are warranted against any other football official'.
"I also note with satisfaction that this report confirms that 'President Blatter's conduct could not be classified in any way as misconduct with regard to any ethics rules'.
"I
have no doubt that FIFA, thanks to the governance reform process that I
proposed, now has the mechanisms and means to ensure that such an
issue, which has caused untold damage to the reputation of our
institution, does not happen again."