The result left both sides on four points from two games, two behind leaders Italy who thrashed Lichtenstein 6-0 at home and one ahead of Finland after their 2-0 win in Armenia.
The Armenians and Lichtenstein have no points.
Bosnia took a 2-0 lead through Edin Visca and Pjanic in the opening 15 minutes but Konstantinos Fortounis pulled one back with a penalty and substitute Dimitris Kolovos levelled after Pjanic was shown a straight red card for a reckless tackle on Zeca.
Roared on by a fervent home crowd, the Bosnians made a flying start as Visca steered in a left-footed shot before Pjanic left Greece keeper Odisseas Vlachodimos rooted to his line with a superb free kick from 30 metres.
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Fortounis drilled in his 64th-minute spot-kick after he was tripped by Toni Sunjic and Pjanic turned from hero to villain barely 60 seconds later after a studs-up challenge on Portuguese-born midfielder Zeca.
Bosnia keeper Ibrahim Sehic denied Kolovos with a reflex save in the 77th but was powerless in the 85th as the midfielder drove home an unstoppable header off the underside of the bar after a fine cross from the right by Zeca.
In the day's early fixture, close-range goals by Fredrik Jensen and Pyry Soiri gave Finland victory in Armenia, with both sides missing chances in an action-packed encounter.
(Writing by Zoran Milosavljevic; Editing by Toby Davis)
