Roy Hodgson's men attacked again on 66 minutes and as the Slovenian keeper Samir Handanovic could only palm a deflected Adam Lallana shot out, Welbeck seemed to scuff his left foot return shot into the ground but was delighted to see it bobble into the net to give his side the lead.
Six minutes later and the crowd saw the best move of the match, as neat interplay for once between Kieran Gibbs, Welbeck and Raheem Sterling down the left played in Welbeck who finished neatly under the keeper.
England had all but clinched the points at 3-1 and Hodgson could finally take a breath in relief or so it seemed. Their guests were not quite finished though and as the Three Lions' team seemed to lose their focus, a shot from the edge of the box had Hart diving to his right but fizzed just too high. Slovenia came close again in injury time but England held them out and took their fourth successive group win.
England would have been unhappy at a poor challenge in the first- half from Cesar who seemed to catch Lallana flush in the face with his forearm, but the officials missed the indiscretion.
They were also forced into a change of personnel before the match as left-back Leighton Baines picked up a hamstring injury, giving an opportunity for Gibbs. With Southamption's Nathaniel Clyne preferred at right back, it meant that the defence was once again changed from the earlier group matches, leaving many pundits a little concerned with the composition and looking for continuity going forward.
It remains to be seen what personnel Hodgson decides to utilise in the friendly next week against Scotland, with perhaps an opportunity for a look at one of the other goalkeeping options and chances for the in-form Stewart Downing to resurrect his international career and Saido Berahino to make his first senior start. Berahino would be an especially interesting 'call' as big things have been predicted from the Burundi born player, who has been such a star in the under-21 squad and for West Brom this season.