A small group of Greek fans booed while the Bosnian national anthem was being played at Karaiskaki stadium, and later set fire to a Bosnian flag. The traveling fans responded by taunting the Greeks with chants of "Macedonia, Macedonia."
Greece is at odds with the former Yugoslav republic of Macedonia in a 21-year-old name dispute.
Bosnia coach Safet Susic said he made no apologies for his largely defensive game.
"I'm not going to make any excuses for the way we played," he said. "I'm happy with the result. We let the Greeks create chances because we gave the ball away too much."