The 31-year-old, team captain until his arrest on March 31, rescinded his contract saying he did not want the club to be affected in any way by his trouble with the law.
"We reached an agreement to rescind the contract. I don't want San Lorenzo stained by a personal problem of mine," Migliore told reporters.
"I'll sit down with my family and see what I do with my life," he added after a meeting with club president Matias Lammens on Thursday night.
"It was difficult for Pablo to stay on at the club given how the (judicial) case developed," Lammens said.
"We've managed a good departure (for Migliore). There would have been an uncomfortable situation for everyone (otherwise)."
Migliore was suspected of aiding an alleged high-ranking member of Boca Juniors' hard core barrabrava fan group wanted by police for his alleged role in the death of a man who died from injuries sustained in a 2011 beating.
San Lorenzo, one of Argentina's so-called Big Five clubs, are sixth in the "Final" championship standings with 20 points from 13 matches after last Saturday's 3-0 home win over Boca Juniors.