Benjamin Sal Llargues tendered his resignation to the Supreme Court of Buenos Aires province, a source at the court told AFP.
The other author of last month's ruling, Horacio Piombo, resigned from the bench on Monday.
Their ruling triggered an uproar in Argentina, with President Cristina Kirchner's chief of staff lamenting "we're in the hands of morons."
It is now up to the provincial governor Daniel Scioli, who is running for president in October, to decide whether to accept the resignations. If he does, the judges will avoid impeachment proceedings in Congress.
In their ruling, the judges reduced convicted child abuser Mario Tolosa's sentence from six years to three years and two months. He had been convicted of aggravated sexual abuse.
They reasoned that, because the six-year-old victim had previously been sexually abused by his father, he could not be a victim of aggravated sexual abuse a second time.
They added that "it is clear that the minor's choice of sexual orientation... would already have been made," as shown by his "transvestism," which they said had to be taken into account in judging the severity of Tolosa's crime.
Tolosa, the vice president of a neighborhood soccer club in Buenos Aires, was convicted of abusing the boy in the club's bathrooms in 2011.
The judges have a record of making rulings considered discriminatory, but until now there had never been a generalized outcry against them.
This time is different.
Piombo has also resigned from his post as a university law professor in Buenos Aires province.
Sal Llargues was relieved of a university teaching position and a spot on judicial oversight board
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