Uruguayan Adrian Leiza, vice-president of the South American confederation's (CONMEBOL) disciplinary committee, said the executive committee's ruling was politically motivated.
Argentine club Boca had been ordered to play eight games without their supporters after an incident in May when fans attacked players of arch-rivals River Plate with mustard gas during their Copa Libertadores clash in Buenos Aires.
The controversy is the latest blow to the South American confederation, which has been swept up in the scandal surrounding world governing body FIFA.
U.S. indictments against 41 defendants, including senior soccer officials from South and Central America, include schemes that involved hundreds of millions of dollars in bribes and kickbacks sought for marketing and television rights to tournaments and matches.
CONMEBOL's headquarters in Paraguay were raided last month after a request for cooperation from U.S. justice officials.
On Monday, FIFA said it had cut off funding to the corruption-hit confederations for soccer in the Americas.
Leiza told Argentine broadcasters TyC Sports that he had resigned following the decision to reduce Boca's ban.
"It was a political decision adopted by the executive committee ... It was adopted in violation of CONMEBOL statutes,” Leiza said. “It’s an illegitimate resolution."
In its original decision, CONMEBOL threw Boca out of the tournament, hit them with a $200,000 fine and ordered the club to play four home games behind closed doors and another four away without their fans in continental competition.
“In the statutes ... there is no provision for granting this kind of pardon,” Leiza said. “I think there is political influence in all areas, in football too, some are more powerful than others, it’s not good.
“It doesn’t do football any good and less at this time with what South American and world football is going through."
CONMEBOL, which had a new president, Paraguayan Alejandro Dominguez, and board voted into office last month, said Tuesday’s ruling was part of its efforts to mark its centenary year. Several other clubs also received reprieves for punishments handed down last year.
“The measures were taken solely and exclusively ... on the occasion of the centenary of the South American Football Confederation,” CONMEBOL said in a statement.
The reduced ban means Boca will play one home match behind closed doors and an away match without their travelling fans.
Fellow Argentine club Rosario Central had a one-match stadium ban for crowd violence during a Copa Sudamericana match lifted.
(Reporting by Mariel Cristaldo, writing by Rex Gowar, editing by Peter Rutherford)
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