That score has added importance as it took United level at the top of the table with Manchester City on goal difference - plus 14 - as well as points, 13.
Everton have now not won in the league since the opening day of the season and are winless in 12 league matches away from home for the first time in 13 years.
For United, they are evolving quickly into a post-Rooney team with the focus on Lukaku.
Rooney was afforded a respectful return.
"Welcome back No 10 Wayne Rooney," had called the stadium announcer.
Within four minutes, though, Rooney was stung as Antonio Valencia scored the kind of goal his former team-mate used to strike to give United an early lead.
Nemanja Matic swept the ball across the front of the penalty area, it took one bounce and sat up invitingly for Valencia to strike a wonderful half-volley that tore past goalkeeper Jordan Pickford. It was only Valencia's second goal since January 2014.
Lukaku should have killed the contest when he was put clear by the impressive Juan Mata. Lukaku checked, to lose Ashley Williams, but then somehow steered his shot wide of a post.
But Everton survived for a time; United became careless. But warnings were not heeded by Everton.
Lukaku set up the unmarked Henrikh Mkhitaryan to score, Matic's shot ricocheted and fell to Lukaku who scored home and Anthony Martial finished things off from the penalty spot.
United were top with Rooney looking on forlornly from the dugout. At least he was already off the pitch by then.