Brazil international Vinícius Júnior scored the decisive goal in the 50th minute with a superb right-footed strike to hand the Spanish side the advantage.
Moments later, he was booked by French referee François Letexier for allegedly provoking the crowd, sparking tensions between both sets of players. The match was suspended for 15 minutes in line with anti-racism protocols after Vinícius reported being subjected to racist abuse, reportedly from Benfica’s Argentine player Gianluca Prestianni.
In the closing stages, Benfica coach José Mourinho was sent off for protesting against the referee.
The return leg will be played next Wednesday in Madrid.