Rooney was the hero for Everton, as he netted the only goal of an intriguing game to hand his side all three points at St. James’ Park.
Newcastle were quickest out of the blocks with Javi Manquillo causing some problems early on for the Toffees with his wide runs, although Ashley Williams was on hand to hack his cross clear on six minutes.
Everton had their first sight of goal on 12 minutes as Idrissa Gueye fired just wide after some good approach play from Aaron Lennon and Jonjoe Kenny.
Williams then dealt with a superb Matt Ritchie ball on 19 minutes before Jordon Pickford gathered relatively comfortably from a Ritchie shot moments later.
Ritchie then hit the woodwork and as luck would have it, Everton went up the other end and scored, as Rooney slotted home from close range after Karl Darlow missed his clearing header at the back post.
Deandre Yedlin saw his 36 minute shot blocked as Newcastle looked to respond, while a Mikel Merino came back off the Everton goal frame.
Newcastle ended the half strongly with Everton on the back foot, but Pickford wasn’t troubled by a Dwight Gayle shot at the end of the first half.
While the visitors looked intent on building on their goal as the two sides emerged for the second half, it was Florian Lejeune who came close to an equalizer for Rafa Benitez’s side. He was inches away to connecting to a Mohamed Diame ball to the back post on 54 minutes.
Rooney was well off target from range before Mason Holgate blocked a Shelvey effort with 63 minutes on the clock.
And try as they might, Newcastle were just unable to break down a newly-resilient Everton side.
Merino saw his 67th minute shot easily plucked out of the air by Pickford, while Gylfi Sigurdsson fired over from a set-piece at the other end.
Darlow expertly tipped a Williams header around his goal before a less impressive effort from Christian Atsu as Everton entered game-management mode by seeing out the game with relative ease before Shelvey picked up his second booking of the night deep into injury-time for a tackle on Gueye.