The Brazilian, who replaced the ineffective Luka Jovic, fought to win the ball back on the edge of the area and then saw the it bounce into his path from a Valladolid defender and kept his composure in front of goal.
"I'm happy with the goal and happy with what he did," Real Madrid manager Zinedine Zidane said about Vinicius. "I'm happy in general, with the introduction of Marco [Asensio] and [Dani] Carvajal too. When we make changes it's to change something, and we did it."
The Spanish champions, who lost Eden Hazard to injury on the day of the game and were also without midfielder Toni Kroos, again lacked fluidity and sparkle in their third outing of the season but just about deserved the win.
"The first half was difficult. We played the same system as last time. In the second half [Zidane] changed the shape, brought on Asensio and I, and we managed to change the game... We know that if we keep clean sheets, we can win games whatever happens. We have a lot of players who can score goals," said Vinicius.
Serbian forward Jovic had forced two smart saves from Valladolid keeper Roberto Jimenez while Casemiro rattled the underside of the crossbar moments before Vinicius struck, while Luka Modric hit the post in the closing stages.
Valladolid keeper Jimenez cursed the defensive slip which allowed Vinicius to score.
"We were very solid throughout the game which is how we wanted to be but against Madrid you always pay a heavy price if you make any mistakes," he said.