The incident occurred in the fourth inning when Young hit Lee with a pitch. As Lee made his way to first, the two players met in the baseline with the Cubs' first baseman throwing the first punch, triggering a bench-clearing brawl. Young also threw a punch.
Both players were ejected from the game as were San Diego pitcher Jake Peavy and Chicago batting coach Gerald Perry.
Perry got a three-game suspension and undisclosed fine for his role in the outbreak.
"I didn't throw at him and that's as far as I'll go," said Young. "I didn't try to hit him and it has nothing to do with anything in the past. I just threw a pitch and it hit him."