Manchester United have not lost the knack of pulling the fat from the fire in the closing seconds of a game. The stadium announcer had just confirmed there would be three minutes of stoppage time when Marouane Fellaini gathered a knockdown from Romelu Lukaku, turned as he held off Loris Benito and stabbed a low shot into the bottom corner.

In doing so he turned the drabbest of scoreless draws into something marginally more memorable, not least because United’s late winner means they will accompany Juventus into the knockout stage. Both sides progressed from Group H as a result of Juve’s win in Turin – until Fellaini struck, United would have had to travel to Spain for their final game with only a three-point lead over Valencia.

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Sir Alex Ferguson always used to say United liked to make life as hard as possible for their manager, and clearly they are still at it, though one often wonders whether José Mourinho himself is also fond of elaboration and over-complication. He certainly spent his evening playing to the cameras on the sideline, reacting to Fellaini’s late winner by hurling a crate of water bottles to the floor.

“This is the Champions League, there can be no room for complacency,” he had said beforehand. “No thinking that the job is done because we have beaten a super team in Juventus, or because we beat the Young Boys in Berne on matchday one.” It is probably about time the United manager sent out some clear, unequivocal messages to his players, even if he risked undermining his own words by starting with Paul Pogba and Lukaku on the bench and selecting Phil Jones in defence for the first time since the Derby County fiasco back in September. “Every player needs to perform properly,” Mourinho continued. “If we play like we did against Crystal Palace we will not win the game.”

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United showed six changes in all to the side held at home in the league by Palace at the weekend, with Antonio Valencia and Fred, the Brazil midfielder, also coming in from the cold.

Mourinho could be seen shaking his head on the touchline five minutes into the game, when Marcus Rashford missed the first opportunity to prevent another scoreless draw. Timing his run well and outpacing Steve von Bergen to reach the edge of the area with only the goalkeeper to beat, Rashford was if anything guilty of overconfidence in his finish, shooting early but managing to clear the bar as well as David von Ballmoos. Fred fired narrowly over as the home side tried to establish an early lead, before Rashford brought a save from Von Ballmoos after being slipped in by Fellaini.

Facebook Twitter Pinterest José Mourinho reacts to Fellaini’s late winner by throwing a crate of bottles to the ground. Photograph: Carl Recine/Action Images via Reuters

A quick goal might have settled the home side’s nerves, as it was they were caught so badly put of position when Young Boys launched a counterattack that Nemanja Matic and Valencia were both booked for separate fouls. Perhaps there was no reason for United to be nervous after beating their opponents convincingly in Switzerland, but Mourinho’s reaction to the Palace disappointment included the advice to stay at home and watch on television if they could not cope with the pressure at Old Trafford.

Whatever the reason, by the half-hour mark the game had settled into a familiar pattern, with United doing most of the attacking but lacking the inspiration or quality to make their superiority count in the final third. Jesse Lingard and Anthony Martial both surrendered possession through untidy passing, as did Fred, who after a bright start had to keep dropping deeper to try and make something happen.

Typical of United’s frustration was an incident shortly before the interval when Rashford surged powerfully through an attempted tackle by Von Bergen on halfway. It was a promising opening and the crowd stirred as Rashford broke forward, only to see him pause and change direction as he waited for support to arrive.

None did, and though Rashford twisted and turned in the penalty area he was eventually dispossessed by Von Bergen, the defender he had originally left stranded 50 yards further back. It was a similar story when Rashford popped up on the left in United’s last significant attack of the first half. He did well to stride into the area and make it to the goal-line, and had the right idea in cutting the ball back for Fellaini to shoot – it was just that the pass missed its intended target by several yards.

Kevin Mbabu gave United a scare at the start of the second half, finding a way past Jones to shoot into the side-netting, just before Rashford did the same at the other end, this time from a situation where either he or Martial should have scored.

Again Mourinho’s reaction was to turn his back and look exasperated, a feeling the ground shared when Fellaini failed to take advantage of a mistake by the Swiss side’s goalkeeper and hooked over the bar from close range.

With just under half an hour remaining Mourinho sent on his two most expensive substitutes, Pogba almost immediately creating a chance from which Rashford should at least have hit the target.

Lukaku set up Martial minutes later with the same result, and United were mightily relieved when a hitherto unemployed David de Gea responded quickly to stop a deflected shot from Ulisses Garcia right on the line. The game still looked like remaining scoreless all the way to its end, yet with their last attack United found a way through.