United started well but after missing two clear chances, it was Barcelona who picked up from where they left at Old Trafford as Messi opened the scoring minutes after Barcelona were denied a penalty by VAR.
Messi would then add his second for the night following David De Gea's rare mistake. Philipe Coutinho's second half goal all but sealed United's fate as Barcelona won four nil on aggregate.
Messi had not scored at the quarter-final stage of this competition since April 2013 against Paris Saint-Germain – although he has had 50 shots in the interim – but he made up for it here.
As for Philippe Coutinho, any thoughts that he may regret his move from Liverpool, were overwhelmingly countered. His goal gave the scoreline the emphasis it deserved.
Elsewhere, Ajax Amsterdam continued with their impressive performance beating Juventus at home 2-1 to win 3-2 on aggregate and reach their first champions league semi final since 1992.