The Portugal forward also piled further pressure on Club Brugge manager Scott Parker, whose future in Belgium is looking bleak with his side losing 5-1 in Portugal, 7-1 on aggregate.
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Benfica headed into the second leg of their Champions League last 16 tie with a 2-0 lead, and soon made it game over.
Ramos brilliantly assisted Rafa Silva's opener with some great play off the wing, and then embarrassed the Brugge defence just before half-time as he wandered into the box and finished.
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The 21-year-old later tapped in an Alex Grimaldo cross to make it three, this his third goal of Benfica's European campaign.
Joao Mario and David Neres then completed the rout, before Bjorn Meijer netted a consolation.
Ramos burst onto the scene last season from the Portuguese side's academy and carried his form into the current campaign, earning him a spot at the 2022 World Cup.
He ended up displacing captain Cristiano Ronaldo in the team's line-up, and scored a hat-trick in his first start against Switzerland in the last 16.
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That saw strong links to Man United emerge, with the Premier League side in need of a new centre forward, having signed stop-gap Wout Weghorst in the January transfer window.
Meanwhile there's plenty of trouble at Brugge, with former Fulham and Bournemouth manager Scott Parker heading for the exit door.
Parker was sacked by the Cherries in August following a 9-0 defeat to Liverpool, and was hired by Brugge in January.
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Since then he has a record of two wins in 12 games, with reports that the club's hierarchy are likely to wield the axe once again with the team sinking in the Belgian Pro League.