The Red Devils are second favourites to lift the trophy in May and head to Jan Breydel Stadium on a four-match unbeaten streak in all competitions.
Chelsea will rightly argue that at least two big calls went against them, but Ole Gunnar Solskjaer will not lose any sleep over the manner of the victory.
It is a win that takes the Red Devils up to seventh in the Premier League and now within three points of fourth-placed Chelsea, while fifth place - likely to be enough to seal Champions League football next season - is only two points out of reach.
United also remain in the FA Cup, with a last-16 trip to Wayne Rooney's Derby County on the horizon, but for now all focus turns back to the Europa League after a 10-week absence.
Solskjaer's men won four, drew one and lost one of their matches en route to topping Group L. They fielded 32 different players in the first phase - more than any other side - but this is where the competition starts to become a little more serious.
Brugge are up next for United in their quest to win the competition for a second time in three years, the Belgian club having dropped down from the Champions League after finishing third in a group containing Real Madrid and Paris Saint-Germain.
There is no shame in that, of course, but Brugge last progressed from a Europa League knockout tie in 2014-15, and they are winless in their last 10 meetings with English sides in all competitions.
Philippe Clement's side lead the way at the top of the Belgian top flight and are unbeaten in 13 games. Replicating that form on the European stage is something they have struggled to achieve, however, and this could well be another hurdle that is too large to overcome.
Club Brugge's form (all competitions): DDWWDW
Manchester United's Europa League form: WDWWLW
Manchester United's form (all competitions): LLWWDW
Victor Lindelof is United's only other fitness doubt after sitting out the win over Chelsea through illness, though it is not expected to be serious enough to rule him out for a second game running.
Further forward, Odion Ighalo made his debut from the bench at Stamford Bridge and is in contention to lead the line on Thursday.
There will be a familiar face in goal for Brugge as Simon Mignolet joined on a permanent deal from Liverpool last August.
Club Brugge possible starting lineup:
Mignolet; Mata, Mechele, Deli; Diatta, Vanaken, Balanta, Vormer, Ricca; Dennis, Krmencik
Manchester United possible starting lineup:
Romero; Dalot, Jones, Maguire, Williams; McTominay, Pereira; Greenwood, Fernandes, James; Ighalo
We say: Club Brugge 0-2 Manchester United
United are not likely to name a full-strength side for the trip to Belgium, but whatever team Solskjaer fields should be strong enough to get the job done. Brugge have lost the previous two meetings between the sides and we are expecting a similar outcome in this first leg.
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