The opening exchanges were cautious, with both sides wary of conceding an early advantage.
Kylian Mbappe tested Anatoliy Trubin with a powerful drive from the edge of the area, while the Benfica goalkeeper also denied Arda Guler as Madrid gradually increased the pressure.
At the other end, Tomas Araujo forced a solid save from Thibaut Courtois with a header, and Fredrik Aursnes came closest for the hosts before the interval, stretching Courtois at full length. Vinicius Junior and Mbappe both threatened late in the half, but it remained 0-0 at the break.
The decisive moment arrived when Vinicius cut in from the inside-left channel onto his right foot and curled superbly into the top corner.
The strike, his 31st in the competition, made him the outright second-highest scoring Brazilian in Champions League history. He nearly added a second soon after, only for Trubin to produce a sharp reflex save from a deflected effort.
The contest was halted for just under 10 minutes following an alleged racist remark, believed to have come from a Benfica player, prompting Vinicius to lead his team-mates off the pitch in protest before play resumed.
Jose Mourinho, facing his former club, was later shown a red card as tensions simmered, and objects were thrown from the crowd in the closing stages.
Madrid now return to Spain with a narrow advantage, having won 10 of their last 12 two-legged European ties.
“We cannot make the mistake of considering a team coached by Mourinho out of the game with a 0-1 scoreline,” said Real Madrid manager Alvaro Arbeloa.
“I don’t know if anyone could do that, but it won’t be me. He is already preparing for that match as soon as they entered the dressing rooms, and it’s not a result to relax on.
“Benfica is not a team that will let us take our foot off the gas if we want to beat them. The Bernabeu will await Benfica, and our fans will be on our side, once again becoming a crucial factor.
“If we want to eliminate Benfica, we still have 90 minutes of very good football ahead, just like we played today.”
