The 29-year-old left the Toffees to join Manchester United for approximtalely £30m in 2004, but pulled on the blue shirt again for 25 minutes of the match against Villarreal.
Rooney told Everton's official website: "It was nice to come back here. The fans gave me a great reception which I was delighted with. Most importantly it was a big day for Duncan. He really enjoyed the game and it was nice to see him on the pitch again."
Everton lost the match 2-1.