"I told the players at halftime that we'd done enough. ... Now everything is up to us. We're not looking at what Greece is doing."
The Bosnians travel to Lithuania for their final qualifier next Tuesday, while the Greeks host Liechtenstein.
Susic rested regular starters Senad Lulic, Haris Medunjanin, Miralem Pjanic in the second half.
Greece beat Slovakia 1-0 in Piraeus on an own goal from the visitors in the first half. Goalkeeper Jan Mucha carelessly controlled a pass backward from Martin Skrtel in the 44th minute and let the ball into the net.
"It was a stupid goal and I apologized to the players. Sometimes it will happen to the goalkeeper," Mucha said.
In-form striker Costas Mitroglou missed two second-half chances for Greece which remained level with the Bosnians, with 22 points from nine matches but with a major goal scoring disadvantage in Group G.
The Slovaks picked five yellow cards during the bad-tempered game, while Skrtel scuffled with several Greek players as he walked off the pitch and was given a post-match red card by referee Deniz Aytekin.
"We could have had a better result and I would have preferred to get to the end of the match without the stress of waiting for another goal that never came," Greece coach Fernando Santos said. "We will keep doing what we have to do and wait for the Bosnia result."
Slovakia coach Jan Kozak said constant pressure from the Greeks decided the game.
"We knew they would press us and they did," Kozak said. "Then the goal came and we couldn't come back from that. It's hard to score against the Greeks when they're playing at home."
Earlier Tuesday, Lithuania beat Baltic neighbor Latvia 2-0 in the group's other match in Vilnius, on goals from Fedor Cernych and Saulius Mikoliunas.