Diego Milito converted a penalty in the final minutes after Walter Samuel's header was ruled out for a shirt-tug.
There was also controversy in the media when Ricardo Quaresma was in the starting XI, but Balotelli was in the stands.
"It was my decision and I don't need to justify myself," snapped the Special One.
"I don't understand why there are so many questions about Balotelli. Today I had two World Cup winners on the bench, Patrick Vieira and Marco Materazzi, so why the focus on Balotelli?
"I made my choices, I sent him to the stands and for 90 minutes he was not on my mind."