Madrid were run ragged in the first half by a brilliant Brugge and their speedy striker Emmanuel Dennis, who scored twice at the Santiago Bernabeu and should have completed his hat-trick shortly after the interval.
Instead, Madrid came storming back as Sergio Ramos headed in, before Casemiro claimed a dramatic equaliser in the 85th minute, seconds after Brugge's Ruud Vormer had been sent off for a second yellow card.
"I would like to keep the second half and forget the first," said Zidane afterwards. "The goals we conceded were laughable."
"The match was historic, the point was historic and the way we played was as well," said Brugge coach Philippe Clement.
After losing 3-0 to Paris Saint-Germain two weeks ago in what was Zidane's worst ever loss as coach, Madrid will be relieved to have avoided another defeat that would have left them facing their first ever group-stage exit in this competition.
Hazard 'one goal' from kick-starting Real Madrid career
But there were no celebrations at the final whistle from those in white shirts after a chaotic performance checked any morale and momentum gained following three consecutive victories in La Liga.
"I am not worried about anything," Zidane said. "We know we are in a worse situation in the Champions League but we keep going."
"We have to do more, we have to do better," added Ramos.
Madrid's fans whistled the players off at half-time and Zidane made two changes, replacing Nacho, who was injured, with Marcelo and his goalkeeper Thibaut Courtois, who was ill, with Alphonse Areola, thrown on for an unforgiving debut.
Gareth Bale was left out of the squad completely, with Zidane claiming that both he and James Rodriguez were injured.
Madrid looked vulnerable to the counter-attack from the start and after nine minutes they were punished. Two close offside calls went Brugge's way as Percy Tau was played on by Ramos and then Dennis stayed level with Raphael Varane.
The finish was even more fortunate, the ball cannoning off Dennis' right foot and rebounding off his left, before rolling agonisingly past the wrong-footed Courtois.
Luka Modric wanted a penalty for a clumsy challenge by Clinton Mata and then fired wide after a pull-back from Dani Carvajal. In between, a sluggish Eden Hazard weaved through but lacked the acceleration, or perhaps confidence, to finish the run. It was symptomatic of his night.
Modric, forceful at one end, was then careless at the other as he was robbed by Dennis, who tore beyond the Madrid defence. With only Courtois to beat, Dennis stumbled again but kept his footing to dig out a lifted finish up and into the net.
Defence is king as Madrid go back to basics ahead of Brugge test
Zidane made the double change at half-time but Dennis should have had his hat-trick shortly after as Ramos gave the ball away only for Areola this time to shut down the shot.
Spared, Ramos then gave Madrid hope. Benzema chipped a cross to the back post where the defender, played onside by the left foot of Mata, headed down and in, VAR checking but allowing the goal to stand.
Brugge wavered and Madrid might have equalised when Modric blasted over, with a frustrated Benzema waiting inside him. With six minutes to go, Vormer collected a second yellow card for a late lunge on the excellent Vinicius Junior and from the resulting free-kick, Madrid struck.
Kroos's curling delivery was met by the leaping Casemiro, who headed the ball inside the far post.
There were four minutes left for a winner as Benzema ballooned a shot over and Ramos beat Simon Mignolet to a cross. His header though lacked power and a weary Brugge held on.
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