Avai, who led 2-1 after 40 minutes, had defender Para sent off for a second booking before halftime and Palmeiras equalised in the 55th minute.
However, a penalty by midfielder Caio, his second goal of the match, and a strike from Roberto in stoppage time handed Avai a surprise win on Sunday.
"The responsibility for the substitutions is mine, I was the one who lost," Scolari said.
"We tried and wanted to win and for that reason we made changes which ended up being more effective for our adversaries. Our midfield was open and gave Avai room," he told reporters.
"We still have to build a playing system so we can be calm, winning, losing or drawing the occasional game. We need patience."
Unbeaten Corinthians have 21 points after nine matches, "Flu" 19 and Ceara 18. Avai are sixth with 14, Santos ninth with 12 and Palmeiras 11th also with 12.
