Rooney, who left Everton to join United six years ago, is regularly jeered by Toffees supporters on his return to Goodison Park.
However, that was expected to be ramped up on Saturday following lurid allegations about the England international's private life over the past week.
Sir Alex Ferguson, though, opted against sending Rooney into the lion's den and left the 24-year-old out of his 18-man squad for the eventful 3-3 draw.
"We made a decision simply because he gets terrible abuse here. We don't want to subject him to that," Ferguson told Sky Sports before the game.
However, assistant boss Phelan later suggested that there were other considerations in the decision not to take the 24-year-old back to Merseyside.
"Wayne wasn't ready to play so we didn't play him,'' he told BBC Radio 5Live.