The Three Lions were already assured of a place in the last 16 but were booed off in Cologne and can expect more criticism after failing to improve on underwhelming performances in edging past Serbia and drawing with Denmark.
England will have to wait until Wednesday's final group games to find out which of the four best third-placed teams they will face in the last 16.
But more questions will be asked over one of the favourites' ability to end a 58-year wait for major tournament glory as a star-studded forward line was snuffed out by Slovenia.
Gareth Southgate made a statement with his team selection, resisting the calls to make mass changes as Conor Gallagher replaced Trent Alexander-Arnold in the only alteration from the opening two games.
If the England boss was looking for a reaction by showing faith in the other 10 who have started all three matches in Germany, he was left disappointed.
Slovenia are now nine games unbeaten, which included beating Portugal 2-0 in a pre-tournament friendly.
Declan Rice had highlighted Benjamin Sesko as their big threat on Monday.
Sesko could have been lining up alongside Rice at Arsenal next season had he not shunned interest to extend his contract at RB Leipzig.
The 21-year-old shrugged off a thigh injury to start and had the first chance of the game when he tamely headed straight at Jordan Pickford four minutes in.
It took 20 minutes for England to pose a serious threat and only the offside flag denied them a slick opening goal.
Rice picked out Phil Foden's run but the Manchester City midfielder had strayed beyond the Slovenian defence before squaring for Bukayo Saka to tap in.
England's lack of attacking threat down the left had been pinpointed as a major weakness against Serbia and Denmark.
Newcastle right-back Kieran Trippier has had to deputise on the left side of defence due to Luke Shaw's lack of match fitness, while Foden tends to drift inside.
However, it was down that side that Southgate's men looked most threatening as a teasing Trippier cross just evaded Gallagher and Harry Kane at the back post.
Southgate took action at the break as Gallagher was replaced by Kobbie Mainoo.
The 19-year-old added some much needed thrust to the England midfield but they still struggled to turn dominance in possession into chances.
Kane saw a header cleared by Sesko from a corner and Rice flashed a shot wide from the edge of the box.
Southgate answered the call to give Cole Palmer his first minutes of the tournament in the final 20 minutes.
The Chelsea midfielder, who scored 26 goals at club level this season, had England's only shot on target of the second half but failed to seriously test veteran goalkeeper Jan Oblak.
A point was jubilantly celebrated by the Slovenians as it did enough for them to progress as one of the best third-placed sides thanks to three draws from their three games.
Matjaz Kek's men missed out on second place in the group solely due to Denmark's superior record in qualifying as the sides had the same points, goal difference and goals scored.
