Yakub Memon was hanged at a prison in the western state of Maharashtra at around 6.30 a.m. local time, Indian Home Ministry spokesman Kuldeep Dhatwalia told CNN Thursday.
In the hours before the execution was carried out, a group of prominent lawyers contacted India's chief justice to seek a postponement of Memon's hanging for two weeks -- a day after Indian President Pranab Mukherjee rejected a final plea for mercy. They argued this was the minimum period of time required between the final appeal and execution.
In an unprecedented move, the Supreme Court held a special early-morning session to discuss the request before rejecting it, Dhatwalia said.
Memom died on his 53rd birthday.
He was originally sentenced to death in 2007 as a key conspirator behind 12 blasts that ripped through several hotels, marketplaces and buildings in Mumbai on March 12, 1993.
According to the Indian prosecution team, those assaults were ordered by the local underworld in revenge for the demolition of a 16th century mosque in northern India by Hindu zealots.
The mosque's destruction triggered a wave of religious violence that left hundreds dead.
Meanwhile, Amnesty International has condemned India's use of the death penalty as a symbol of its resolve to tackle crime.
"This morning, the Indian government essentially killed a man in cold blood to show that killing is wrong," Aakar Patel, Executive Director, Amnesty International India, said in a statement.
"This execution will not deliver justice for the 1993 Mumbai blasts. It is a misguided attempt to prevent terrorism, and a disappointing use of the criminal justice system as a tool for retribution."
In 2006, popular Bollywood star Sanjay Dutt was also convicted of acquiring illegal weapons tied to the Mumbai bombings. He was, however, cleared of a more serious charge of conspiracy in the attacks.
Public Prosecutor Ujjwal Nikam said 100 of 123 suspects were convicted for their roles in the bombings, one of the longest-running trials of a terrorism case in the country.
Memon was among 11 prisoners sentenced to death by the trial court. The other 10 appealed their sentences, which were commuted to life in jail in 2013.