After a goalless first leg, Barcelona knew a draw would not be good enough to make it through to the quarter-fnals.
The Argentine ace made no mistake from 12 yards with a cheeky panenka before Philippe Coutinho doubled their adavantage.
However, Lucas Tousart pulled one back for Lyon on the hour mark to leave the tie in the balance.
But Messi restored their two-goal cushion before Gerard Pique and Ousmane Dembele sealed their spot in Friday's draw.
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