Despite playing the majority of last week's first leg with 10 men following an early red card for Pau Cubarsi, Barcelona picked up a 1-0 win and entered the return match as heavy favourites to progress.
Just 11 minutes into the second leg, Yamal got the ball and weaved his way past a couple of defenders before picking out Raphinha at the back post, with the Brazilian attacker making no mistake from close range.
Benfica kept their hopes alive when Nicolas Otamendi equalised on the night two minutes later, but Yamal took centre stage once more in the 27th minute.
This time he received the ball by the touchline before cutting inside and whipping an unstoppable effort past the goalkeeper.
At 17 years and 241 days old, Yamal became the youngest player in Champions League history to score and assist in the same game.
Raphinha then gave Barcelona further breathing space by scoring again three minutes before the interval.
But his second goal of the evening was not without controversy, as it was initially ruled out for offside.
After the flag went up, the referee brought play back for a foul in the build-up and booked Otamendi.
However, VAR subsequently determined that Raphinha was onside and the goal was eventually given, while Otamendi's yellow card was rescinded.
There were no further goals as Barcelona cruised to a 4-1 aggregate victory.
Yamal now has 12 goals and 17 assists across all competitions this season after winning the Euros with Spain last summer.
The teenage sensation appears to be going from strength to strength as Barcelona chase down their first Champions League triumph in a decade.
Barcelona will face either Borussia Dortmund or Lille in the last eight.
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