His goal, a stunning strike into the top corner after a surging run in off the left, ensured Sevilla took nothing from a game they had dominated for most of the first half.
Rafa Mir headed them in front early on but the game turned on an error from goalkeeper Bono, who gifted Karim Benzema his 19th goal of the season, the night before the 33-year-old hopes to win the Ballon d’Or.
Victory sends Madrid four points clear of Real Sociedad, who they face at Anoeta next weekend, while Sevilla stay fourth, now five points off the top.
"Maybe a draw would have been a fairer result but I don't think we deserved to lose," said Ancelotti.
Real Sociedad lost ground after slipping to a surprise 1-0 defeat by Espanyol before Atletico Madrid bounced back from their Champions League loss to AC Milan in midweek with a thumping 4-1 win away at Cadiz.
Vinicius now has 11 goals in 24 appearances this term and while he was never a guaranteed starter under Zinedine Zidane, the Brazilian has exploded into life under Carlo Ancelotti.
This was the kind of decisive moment Madrid hoped they would be getting from Eden Hazard but with the Belgian still lacking both form and fitness, it seems they now have a ready-made replacement.
"I knew about his individual qualities, his dribbling, in one against ones, his speed, in all that he's very strong," said Ancelotti. "But what surprises everyone now is that ability to score goals, which he didn't have before.”
Madrid were sluggish and sloppy for most of the first half an hour, livened up only by Benzema’s goal that was gifted to him after Bono’s mistake.
Sevilla took the lead in the 12th minute when Mir was allowed acres of space to plant a header past Thibaut Courtois.
They should have been two ahead as David Alaba cleared off the line from Mir, who then forced an excellent save from Courtois after a lethargic touch from Toni Kroos gave him a second chance.
Lucas Ocampos struck the crossbar after Sevilla swarmed forward again but in the 32nd minute, they handed Madrid a lifeline as Eder Militao’s shot from distance squirmed through the hands of Bono, came back off the post and to the feet of the grateful Benzema.
Madrid were buoyed by the goal and Marco Asensio went close with a curled finish over the bar while Sevilla thought they should have had a penalty when Alaba toppled Ocampos in the box.
The second half drifted, with neither team for a while willing to over-commit. Vinicius Junior tore away on the counter-attack but blazed over and Madrid moved into the ascendancy in the last quarter of an hour, with Sevilla happier to hold on for a point.
Alaba volleyed over before Vinicius took centre stage. He was almost on the left touchline when he chested Dani Carvajal’s cross-field ball inside Ocampos before darting past Gonzalo Montiel and unleashing a stinging shot that hit the top corner.
Atletico Madrid had earlier blown away Cadiz, with Diego Simeone's side scoring all four of their goals in the second half.
Thomas Lemar began the scoring in the 56th minute before Antoine Greizmann and Angel Correa put Atletico out of sight. Jan Oblak's own-goal pulled a goal back for Cadiz but Matheus Cunha responded immediately to add a fourth for Atleti.
Victory helps lift morale after Atletico's 1-0 defeat at home to AC Milan that leaves them with a mountain to climb to reach the Champions League last 16.
Atletico look better placed in La Liga, sitting second in the table and above Real Sociedad, after their loss to Espanyol.
La Real could have gone top for a few hours at least, but instead saw Espanyol end their 13-match unbeaten run in the league thanks to Yangel Herrera's late winner.