A bench of Justices P C Ghose and Amitava Roy issued notice to Baig and sought his reply on the plea of the state government.
The plea had challenged the March 17, 2016 judgement of the high court which also acquitted Baig from serious charges under various sections of the Unlawful Prevention (Activities) Act and IPC, including sections 302 (murder) read with 120-B (criminal conspiracy).
Baig, who was alleged to be a member of banned terror outfit Indian Mujahideen, was arrested in September 2010 from Latur in Maharashtra for involvement in the blast at German Bakery, a popular eatery in Pune's Koregaon Park area, which killed 17 persons and injured 58, including some foreigners.
In 2013, the trial court had convicted and awarded him capital punishment.
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"Prosecution witness 93 was the autorickshaw driver who saw the respondent (Baig) with the planter of the bomb which proves the last seen theory. In the test identification parade the autorickshaw driver identified the respondent (Baig).
"In spite of that, the high court held that the plea of the prosecution that the respondent was last seen with planter of the bomb does not gets credence," it said.
Besides Baig, Qateel Siddiqui was also arrested in the case, but he had died in Pune's Yerawada jail following a scuffle with other inmates.
The other wanted accused are Indian Mujahideen operatives -- Mohsin Choudhary, Riyaz Bhatkal, Iqbal Ismail Bhatkal, Fayyaz Kagzi and Sayyad Zabiuddin Ansari.
Yasin Bhatkal,, who had allegedly planted the bomb in the eatery, was arrested in August 2013. The case against him is pending before the trial court.