Over the past week, as the execution approached, a robust debate erupted here over whether Mr. Memon deserved to die. That debate gathered strength on Wednesday as India’s president rejected his final plea for mercy. By late Wednesday night, several hundred people opposed to Mr. Memon’s execution had gathered for a candlelight vigil at Jantar Mantar, a giant sundial that is this city’s preferred rallying point for public protest. Not until 5 a.m. on Thursday did India’s Supreme Court deny Mr. Memon’s final appeal.

The debate was fueled by last-minute questions about Mr. Memon’s supposed cooperation with investigators, by concerns about the treatment of Muslim defendants in India’s courts and by the uncontested fact that the actual masterminds of the bombings remain at large.

This week, as Mr. Memon’s execution began to appear more likely, Muslim leaders and some legal experts argued with increasing vehemence that India’s death penalty was applied more aggressively against Muslims and other minority groups.

“Yes, Yakub was involved, but he did not deserve capital punishment,” Asaduddin Owaisi, a Muslim member of India’s Parliament, told reporters here on Wednesday. He cited cases of non-Muslim defendants convicted of heinous crimes who have avoided execution. The debate even embroiled Salman Khan, one of India’s biggest movie stars, who on Sunday posted a series of messages on Twitter that seemed to imply that Mr. Memon was being hanged for the crimes of his older brother, Ibrahim (Tiger) Memon, who prosecutors say is one of the masterminds still at large. “Brother is being hanged for Tiger,” Mr. Khan wrote, only to retract his posts a short while later after facing heavy criticism, including from his father.