Sky and the BBC reported that, barring any late injuries, manager Gareth Southgate had decided to name the Manchester United striker among the substitutes for the game in Ljubljana.
Southgate was due to give a news conference later in Slovenia.
Rooney is England's most capped outfield player, with 117 appearances, and all-time top goalscorer but his recent indifferent form has attracted criticism.
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He has scored just once in 12 games this season and only once in the last seven internationals.
The 30-year-old was jeered by some in the 82,000-strong Wembley crowd towards the end of England's 2-0 win over Malta on Saturday and that reaction triggered a lively debate among England supporters about his future role.
Slovenia coach Srecko Katanec said he hoped Rooney would not be playing against his side.
"Wayne Rooney is a leader of this team, he has the experience a captain needs and it is quite hard to substitute him or leave him out," the BBC quoted him as saying.
"Because of his experience and quality I would rather he would not start than he does start."
Southgate, who took over after the departure of Sam Allardyce last month, defended the player - who started as captain against Malta - and said his experience was crucial to the team.
"I think his experience, his leadership has been crucial throughout this week, not just today," Southgate said on Saturday.
"Every debate seems to focus on him, the onus on him is enormous and the criticism of him is at times unfair. He ploughs on and plays with pride and captains his country with pride."
Rooney has been a substitute in Manchester United's last three games and has also been deployed in a deeper role for England, who have a 100 percent record in qualifying Group F.
Southgate has Jamie Vardy, Daniel Sturridge, Theo Walcott and Marcus Rashford among striking options while Eric Dier, left out against Malta due to a hamstring problem, is likely to return in midfield alongside Jordan Henderson.
Rooney and the rest of the England squad trained at Tottenham Hotspur's Enfield facility on Monday.
(Reporting by Alan Baldwin, editing by Ed Osmond)
