Interim manager Gareth Southgate has chosen to leave his captain out of the starting line-up as anticipated, with Jordan Henderson taking the armband.
Rooney's demotion is one of two changes to the side which defeated minnows Malta at Wembley on Saturday.
Eric Dier replaces the Manchester United forward, while Danny Rose comes in for the injured Ryan Bertrand at left-back.
Southgate confirmed that Rooney would be among the substitutes on Monday, claiming that it was a tactical decision on his part to omit the 30-year-old.
He said: “It is very straightforward. We’ve looked at Slovenia, the way they play and the profile of midfield that we wanted to play, what was needed for this game.
“In no way is it a reflection on Wayne’s performance on Saturday. In fact, we were very pleased with what he did; we knew he would have a lot of the ball, he dictated the game, and played with great tactical discipline.
“Of course, it was not an easy decision to take because of the respect I have for him as a player, as a person and as a captain of this team. We felt it was the right decision to go with the team that we’re starting with.”
England: Hart, Walker, Stones, Cahill, Rose, Dier, Henderson, Walcott, Alli, Lingard, Sturridge.
Substitutes: Forster, Pickford, Gibbs, Antonio, Smalling, Keane, Vardy, Rashford, Townsend, Oxlade-Chamberlain, Rooney.
Slovenia: Oblak, Struna, Samardzic, Cesar, Jokic, Krhin, Kurtic, Verbic, Birsa, Bezjak, Ilicic.
Substitutes: Skubic, Jovic, Crnic, Novakovic, Belec, Trajkovski, Koprivec, Mevlja, Kronaveter, Zajc, Pihler, Omladic.Reuse content