Manchester United are through to the Europa League knockout stage courtesy of Henrikh Mkhitaryan’s fine first goal for the club and Zlatan Ibrahimovic’s late finish. José Mourinho’s team finished second in their group, however, so will be unseeded in Monday’s draw for the round of 32.

A first away win in the competition was marred by an outbreak of violence during the interval, moreover, and there was disappointment for Wayne Rooney, who remains stuck on 248 goals and still in need of two more to become the club’s all-time record scorer.

Of his goal, Mkhitaryan said: “I think it can be weight off your shoulders – I’ve been waiting a long time for this goal. My next goal has to be at Old Trafford – I want to score at home.

“We had a strong second half, it was better than the first half – we weren’t playing well in the first period – we couldn’t understand each other. The second half, it was opposite. We played very well.”

United’s prime concern had been to secure the draw required to seal a place in February’s next phase. They started confidently and in control against the side from the Donbass region of Ukraine, 550 miles away from where the game was played in Odessa. This featured Paul Pogba, Juan Mata, and Ander Herrera teasing their side forward from inside Zorya’s half, though the first clear chance was actually fashioned by the Ukrainian club as Ihor Kharatin forced a smart save from Sergio Romero to his right.

From here it was all United for a prolonged passage. Herrera swung a left foot volley at the goalkeeper Ihor Levchenko, Pogba shot wide and a Herrera cross found Pogba’s head but he failed to finish. Daley Blind took a corner from the left that was flicked on by Pogba towards Ibrahimovic and another corner was won. As is the story of United’s Premier League campaign, at this point they lacked the killer touch in front of goal.

On the half-hour a firecracker was thrown near Romero that gave off a loud bang and appeared to disconcert the Argentinian. This followed Blind having to complain to officials about a laser pen being shone on to his face.

Mourinho’s men were not helped by a pitch that was bobbly and cut up due to rain and a thaw at the stadium situated on the banks of the Black Sea. That followed the early doubts regarding whether the match could be played due to the ground being frozen on Wednesday.

Beforehand Mourinho had rated the surface as “not too bad – I don’t think it’s dangerous”. Afterwards a contented Mourinho praised the efforts of the local groundstaff. “The pitch was better today than yesterday and good enough to pay football on and we appreciate the efforts to give us a good pitch,” he said.

The manager made six changes from Sunday’s frustrating draw at Everton. Out went David de Gea, Anthony Martial, Phil Jones, Matteo Darmian, Antonio Valencia and Michael Carrick. In came Romero, Eric Bailly, Mata, Rooney, Ashley Young and Blind.

Of note here were the returns of Rooney, after he was suspended for Sunday, and Bailly, a first-choice centre-back until the knee injury that caused the Ivorian to miss nine games, having last featured in the 4-0 loss at Chelsea on 23 October.

Of his return Mourinho said:“It’s important, I think [Phil] Jones and Marcos [Rojo] did five good matches in a row so but they can’t always do it – just those two. Having Eric back, albeit for just two weeks before he goes to the Africa Cup of Nations, allows us to rotate a little before Christmas.”

After a becalmed period it was Bailly who at last managed to fire at goal, though his overhead kick lacked power and Levchenko collected. By the point the half had petered out and two rare Rooney shots, plus a too-high Rojo effort, ended it.

Now came the fighting as two United flags appeared to be taken by rival fans from the travelling supporters’ section to the left of what was Zorya’s goal in the first half. This caused a chase and scuffles before the flags reappeared behind the other goal, where a flare was lit in celebration.

As this was settling down United took the lead via Mkhitaryan’s superb solo effort as he weaved his way towards Levchenko then left him no chance. His first United finish was also only their second on the road in the competition. With Feyenoord also losing to the eventual group winnes Fenerbahce, United were now even firmer favourites to finish second, so it became an exercise in controlling the contest.

This they did with little threat to Romero as Ibrahimovic collected a 13th of the term on 88 minutes to seal the victory. Now Mourinho and his men can put the competition out of their minds until the spring.