The match raised plenty of questions for Fabio Capello as the likes of Robert Green, Matthew Upson, Shaun Wright-Phillips and particularly Glen Johnson did little to enhance their international reputations.
However, Jermain Defoe continued his excellent start to the season with another goal while Aaron Lennon and Wayne Rooney looked particularly lively.
Tottenham striker Defoe came on as a half-time substitute for Emile Heskey and scored England's second goal with a clinical strike after being set up by Lennon. Dofoe must be knocking on the door to partner Rooney in the starting lineup soon.
Johnson was shown up by Slovenia at regular intervals and the Liverpool man was at fault for the visitors' late goal. He appears to be good going forwards but seems to falter in his defensive duties and against better opposition may struggle to cope.
Robert Green was lucky to escape when he handled the ball outside his area early on in the match in a momentary lack of concentration.
Milijove Novakovic then rounded the West Ham United shot-stopper but could only turn the ball onto the roof of the net after being forced wide.
John Terry headed a corner against the bar before England took the lead 14 minutes before the interval with the softest of penalties.
Rooney appeared to be fouling Bostjan Cesar as the two men tried to get on the end of Steven Gerrard's cross but the referee thought otherwise and pointed to the spot to Slovenia's fury.
Frank Lampard made no mistake with his penalty to give England a somewhat fortunate lead.
The goal preceded England's best spell of the match and Rooney should have doubled their advantage only to fire against the post from three yards out when it seemed easier to score.
Gerrard then shot narrowly wide from 25 yards out but England lost their way at the start of the second period after a host of changes by Capello at half-time.
It was a turgid affair until Defoe's precise 63rd-minute strike briefly enlivened proceedings.
Rooney was denied again with 19 minutes remaining when he turned Lennon's cross goal wards only for Matej Mavricrozic to kick the ball off the line.
Then with five minutes left and the match drifting to a conclusion, Johnson was embarrassed by Nejc Pecnik whose cross was headed home by Zlatan Ljubijankic.
England held on to their narrow advantage but they and Capello will need to step up their game if they are to beat Croatia in Wednesday's World Cup qualifier.