Asahara, 63, a pudgy, partially blind yoga instructor, was sentenced to hang in 2004 on 13 charges, including the subway gas attacks and other crimes that killed at least a dozen people.
Japan's Justice Ministry has confirmed reports that six followers of a doomsday cult have been executed along with its leader.
In total, 12 followers had been on death row with Asahara after members of the cult punctured plastic bags to release sarin nerve gas inside train carriages in five co-ordinated attacks.
That attack, which involved a refrigerator truck releasing the gas to be dispersed by the wind through a neighbourhood, failed to kill the judges but killed eight other people and injured hundreds.
Along with Ashara, Japanese executioners killed two scientists who helped make the gas and one of the men who actually carried out the attack.
Despite the horror that persists over the Aum's subway attack and other crimes, some experts had warned against the execution of Asahara and his acolytes. "However, the death penalty is never the answer", said Hiroka Shoji, East Asia Researcher at Amnesty International. A string of crimes resulted in the deaths of 29 people. All told, 19 cult members, including Asahara, were apprehended and tried for their crimes.
FILE - In this March 20, 1995, file photo, the injured of the deadly gas attack are treated by rescuers near Tsukiji subway station in Tokyo.
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On 16 May, Shoko Asahara was finally arrested.
Under instructions from Asahara, six Aum members strangled 33-year-old lawyer Tsutsumi Sakamoto - who had been helping parents seeking to free their children from the cult's control - as well as his 29-year-old wife, Satoko, and their 1-year-old son, Tatsuhiko, after breaking into the family's home in Yokohama in the early hours of November 4, 1989.
Executions are rare in Japan but surveys show most people support the death sentence.
The executions were a long time coming, but they were expected as the last trial in the case had been completed and some of the condemned convicts had been transferred to other prisons earlier this year.
"The fear, pain and sorrow of the victims, survivors and their families - because of the heinous cult crimes - must have been so severe, and that is beyond my imagination", Justice Minister Yoko Kamikawa told a news conference.
Cult guru Shoko Asahara, left, of Aum Shinrikyo walks with Yoshihiro Inoue, then a close aid, in Tokyo. The cult had plans to attack senior Japanese government leaders, it said.
Asahara told his followers he is the incarnation of Shiva, the Hindu god of destruction and regeneration, and urged them to entrust themselves and their assets to Shiva and himself for life, according to prosecutors who indicted him.
The cult claimed 10,000 members in Japan and 30,000 in Russian Federation.