The 31-year-old has agreed a two-year-deal at Goodison Park after passing a medical on Saturday.
Rooney left Everton for United in 2004 for a reported fee of £27 million ($45.75 million), which made him the world's most expensive teenager at the time.
He went on to win 12 major trophies for the club in 13 years, including five Premier League titles, three League Cups, the FA Cup, the UEFA Champions League and the UEFA Europa League.
He was named captain by Louis van Gaal in 2014 and broke Sir Bobby Charlton's long-standing scoring record at United last season, eventually finishing on 253 goals in 559 appearances.
Rooney, England's record goalscorer, fell down the pecking order under manager Jose Mourinho last season and United's pursuit of Everton striker Romelu Lukaku prompted talk that he would leave before next season.
Rooney is the latest signing in a busy transfer window at Goodison Park, with Davy Klaassen, Jordan Pickford, Sandro Ramirez and Michael Keane secured as the Toffees look to close the gap on the top six.
"Wayne has shown me that ambition that we need and that winning mentality – he knows how to win titles and I'm really happy he's decided to come home," said Everton manager Ronald Koeman.
"He loves Everton and he was desperate to come back. He is still only 31 and I don’t have any doubts about his qualities. It's fantastic he's here."
