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The Young Lions were leading 2-0 at half-time thanks to goals from Conor Gallgaher and Cole Palmer but were dominated in the second period as the hosts claimed a draw.
Poor defending at two set-pieces allowed Slovenia, through goals from Mark Spanring and Dusan Stojinovic, to claim their point.
England had a late chance to steal a win through Emile Smith Rowe but Slovenia were well worth the draw after stunning England with their physical second-half performance - something Carsley had warned his players was coming.
"We started the game really well, I really enjoyed the way we played in the first half," said England’s head coach.
"We created a lot of chances, moving the ball well and playing quickly. There was always the threat of a counter-attack or set play, we made that clear at half-time. Their big threat was set plays.
"It was disappointing then to start the second half how we did. We started a little bit slowly and maybe gave them the momentum. We had opportunities but never really... I never had that feeling we were in control of the game, we were a little bit passive in the way we tried to get after the ball and gave up territory.
"We're still building our reputation as a team and a squad and it's important we take experiences like today, 2-0 up away from home - worst-case scenario you win 2-0. If we build on this result and use it for experience it will be a positive result for us."
England face a trip to Andorra for their third game in this 2023 U21 Euro qualifying group, where they are now five points behind the Czech Republic with a game in hand.