Possibly the best illustration of how toothless England were for long spells of this never-in-doubt victory over the fourth-worst team in Europe was that they mustered their first shot on target only in the 64th minute. It came from Trent Alexander-Arnold and it was routine for the Malta goalkeeper, Henry Bonello.

England had been ahead since Enrico Pepe’s eighth minute own goal, forced by Phil Foden, who was the best player on the pitch. But it was all a bit vanilla, Gareth Southgate’s team not needing to overexert themselves and not doing so.

Qualification for the European Championship finals next summer had already been secured, the jeopardy long since removed from the campaign, and it was difficult to get too angry about the failure to rack up the goals. The massive Wembley crowd did not. They were relaxed as England rather went through the motions.

It is now all but certain that England will be among the top seeds for the group phase draw on 2 December. Only a nine-goal defeat in North Macedonia in the final qualifier on Monday night would deprive them of the target that Southgate had set for this international break.

Harry Kane was incensed to be shown a yellow card for what the referee, Luís Godinho, saw as a 28th minute dive inside the area; it was in seen-them-given territory, the contact with Bonello plainly there. But the England captain could smile after he swept home the second goal following a lovely team move – which stood out, in truth, because of its novelty factor.

Southgate had started with an experimental midfield; Jordan Henderson holding, Alexander-Arnold and Conor Gallagher to the sides and higher up.

Henderson was not great – it was possible to hear boos when he was substituted – while it felt like a missed opportunity for Gallagher. He was withdrawn at half-time. Alexander-Arnold’s passing was a highlight.

It was strange to report but Malta might have scored inside the first minute, Matthew Guillaumier robbing Gallagher and passing to Teddy Teuma, who fizzed a low drive inches past Jordan Pickford’s post. If that was certainly not a part of England’s script, what came shortly afterwards was more like it.

Foden’s first touch, with which he sent the ball up the inside-right channel to chase himself, was typically instinctive and how he chased, flicking on the afterburners to zoom into the area. He thought that the cutback was on but it did not reach Kane, hitting Pepe instead and flying past Bonello. Pepe can say that he scored at Wembley.

Foden brought the tricks and the bursts but it was all too pedestrian from England in the first half, lacking in precision and incision. The crowd made Mexican waves and threw paper planes. Malta let England know they were in a physical contest, even if some of their challenges were a little overzealous while they kept their shape and made a few inroads.

The big talking point came when Godinho chose to ignore Kane’s penalty claim. It was a questionable decision and to caution him was too much. Bonello had taken a heavy touch on a backpass, Kane nipped in and left his trailing leg behind him, waiting for the contact, which duly came.

England needed a lift for the second half and Southgate introduced two of his key men, Kyle Walker and Bukayo Saka, for Fikayo Tomori, who had been asked to play out position at left-back, and Gallagher. Tomori did absorb a couple of heavy tackles. Marc Guéhi was the pick of the England defenders, calm and intuitive throughout.

Southgate’s starting midfield shape represented a slight deviation from his recently trialled 4-2-3-1. The injured Jude Bellingham was missed and so was Declan Rice until he came on as a 61st-minute substitute. It would have annoyed Southgate to see how Malta were able to get around the back of his midfield, at times.

It was not Marcus Rashford’s night. He could get little going and, when he nutmegged Steve Borg, he found himself in a sandwich between the Malta captain and the chasing Joseph Mbong. Down he went but it was no penalty. At least he did not get booked.

The icing on the cake came when Alexander-Arnold took a touch and surged forward only to crash straight into Rashford, who had got in the way. Rashford needed treatment and he would be substituted shortly afterwards, Cole Palmer coming on for his first cap.

Southgate got Foden into a No 10 role after the interval and he was involved in the second goal, looking first-time for Saka after positive approach work from Alexander-Arnold and Walker. Saka then went to Kane with a pass that was as astute as it was unselfish.

Kane did what he does, his 62nd England goal a formality, and Rice would be denied the third moments later. He stormed forward from midway inside the Malta half and, with red shirts backing off, he cut inside and lashed past Bonello from outside the box. Unfortunately for him, the VAR had spotted that the shot had brushed off Kane, who was in an offside position.