Stoppage time began with Sam Allardyce, alone on the edge of his technical area, burying his head in his hands as another of his side’s desperate attacks ran aground. It ended with a spin, grin and two-fisted pump of the air aimed at those members of his coaching staff still on the bench. His assistant, Sammy Lee, had already bounced gleefully beyond him on to the edge of the turf. If nothing else, the new manager has brought England a dash of good fortune.

Allardyce, albeit through a grin, actually put that down to a lucky Slovakian coin he had been given at the team hotel in Bratislava earlier in the day by the father of a boy in a wheelchair. “He asked if it was OK to have a picture taken with his son, and then he gave it to me saying it was ‘lucky’,” he said. “I had it with me in my pocket, we won, so it’ll stay with me from now on.” How Roy Hodgson would have benefited from a similar token in France. This contest could have been lifted straight from Saint-Étienne, a second grim scrap against Slovakia within 11 weeks which had threatened to end in bruising stalemate. Then came Danny Rose’s burst, Adam Lallana’s calm touch and Matus Kozacik’s rare blunder.

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Victory with the last kick of a game can have a cleansing effect, shaping the perception of everything that had preceded it. Distorting it, even. A 13th successive qualifying win, plucked from potentially the trickiest away fixture in Group F, has actually set up England neatly for Allardyce’s two-year journey to Russia. They have early momentum in the section, which feels remarkable given how sluggish so much of their play had been up to the moment Martin Skrtel was dismissed. Allardyce could point to relief, not regret, before the team’s departure.

Yet, certainly for 70 minutes, this had been all too familiar. England had been lifeless where they needed a spark. Harry Kane was horribly isolated, his principal impact to draw the key fouls from Skrtel. Raheem Sterling showed flashes of form but not the prolonged threat he has demonstrated for Pep Guardiola at Manchester City. There was so little front-foot play. It all felt slack, a series of sideways or backward passes. Where was the pace and unpredictability of a Marcus Rashford to slice through the defence? Dele Alli offered some forward momentum from the bench, but England had huffed and puffed as if stuck back at Euro 2016.

The sight of Wayne Rooney in retreat merely laboured the point. The captain became the country’s most capped outfield player here, his 116th international marked with a free-kick bent on to the roof of the net, one desperate appeal for a penalty and complaints when Theo Walcott’s goal was disallowed in the last minute of normal time. He began in central midfield, drifted briefly left, then ended up as an anchor. Again, the fact England won relegates the issue of his role to the periphery, but it is surely a topic for debate. Under Hodgson, the sense was the 30-year-old would always be shoehorned into the side: a scorer in qualification, a midfielder at the tournament stage.

Facebook Twitter Pinterest Wayne Rooney in action during the 1-0 win over Slovakia. Photograph: Dan Mullan/Getty Images

Everything Allardyce said post-match suggested Rooney will be retained regardless of form. It had begun with a television interview in the bowels of the stadium. “Wayne played wherever he wanted,” said the manager. “He was brilliant and controlled midfield. I can’t stop Wayne playing there.”

That demanded further clarity upstairs. “This is the most decorated outfield player in England. He’s won everything at Manchester United, at Champions League and domestic level. I think he holds a lot more experience at international football than I do as an international manager. So, when he is using his experience and playing as a team member, it’s not for me to say where he’s going to play.

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“It’s up to me to ask whether he’s doing well in that position, of course, and contributing. If so, great. We’d like to get him into goalscoring positions more. He’s been a goalscorer all his life and I want him to do that again, but he reads a game as he reads it. He read it very well, we won and dominated. I must admit, he did play a little deeper than I thought he’d play. But I was pleased with his performance.” As a glimpse of what awaits, that was intriguing. Allardyce had bemoaned the slow nature of England’s build-up play, and yet Rooney’s passing can actually be identified as slowing this team down.

Player and manager would argue it can also be the most penetrative, even if it was actually rather too hit and miss in Trnava, but he is a player who needs more energy around him, an Alli from the start. Certainly, it was rather dispiriting to see Jordan Henderson further upfield for so long. That balance did not seem right.

If the management believe this team cannot yet do without Rooney’s experience, then they need to find a way of making him fit more comfortably into the selection. Victory should not mask that reality.