"(The decision) has implications that go beyond sports justice... I have presented my resignation from the post of league president," Herminio Loureiro told the Lusa agency on Thursday.
Loureiro, whose mandate was due to end in May, said he would not run for the post again and would provide more details on the reasons behind his resignation at a later date.
The league handed Hulk the four-month suspension from domestic competitions last month for assaulting a match steward in the players' tunnel after a game against Benfica in December, but Wednesday's decision following Porto's appeal means he is now eligible to play.
The federation also cut Porto defender Cristian Sapunaru's six-month suspension for assaulting stewards in the same game to four games from six months.
Hulk was given a temporary ban straight after the incident and has not played in domestic competitions since, but featured in the ties against Arsenal in the Champions League last 16.
Porto said in a statement that the Brazilian had missed 17 matches since the suspension, calling the disciplinary process "an aberration."
The club added that it has instructed its lawyers to file for compensation from the league.
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