Just as it looked as if Atalanta would hold on for a draw, Mendy received the ball outside the area after a corner and curled a shot into the right side of the net from 20 yards.
The striker, who has netted 17 goals in all competitions this season, has still not recovered from a slight tear in his left abductor muscle.
The hard-fought win came after Atletico Madrid fell at home to Levante 2-0; Barcelona take on Cadiz today.
Madrid's third straight league victory left Zidane’s team five points behind Atlético, which won 2-1 at Granada on Saturday and has two games in hand.
Benzema and Ferland Mendy scored in the second half as Madrid went on to win for the third time in four games in the Spanish league.
Varane scored twice in the second half to help the defending champions come from behind to win at last-placed Huesca 2-1 in the Spanish league on Saturday.
A year and a half later, many in Spain believe Hazard's ill fortune with injuries mean he will never be the star he was in the English Premier League.
Madrid said the 73-year-old Pérez is asymptomatic and tested positive after a routine test. No other details were released.
None of Real Madrid and Barcelona made a deadline day transfer with the latter mired in political turmoil, being led by a caretaker board that can't make many decisions regarding transfers.
Madrid giants lost 2-1 at home to Levante in a match that the defending champions played with 10 men from the eighth minute when defender Eder Militao was sent off.
Odegaard has been at Madrid since 2015 — when he joined at the age of 16 — but failed to establish himself at the Spanish giant
Eden Hazard scored and set up Karim Benzema for his first of two goals as Real Madrid eased to a 4-1 victory at Alavés.
The match at Alavés on Saturday comes after Madrid was dumped from the Copa del Rey by a third-tier side that struck an added-time winner playing with just 10 men.
The announcement came two days after Zidane coached the team in a 2-1 loss at third-tier Alcoyano in the Copa del Rey.
Real Madrid conceded late against its 10-man opponent on Wednesday to squander yet another trophy chance this season.
Alcoyano scored in the 80th minute to force extra time and again in the 115th to shock the Spanish powerhouse and make it to the last 16.
Athletic is looking to win its third Spanish Super Cup title, and first since beating Barcelona in the 2015 final. The Basque Country club also won the competition in 1984.
Griezmann scored a brace and set up Lionel Messi for one of the Argentine’s two goals on Saturday to lead Barcelona to a 4-0 win at Granada.
After a tight first half, Casemiro evening opened the scoring with a 57th-minute header from Marco Asensio's cross and Karim Benzema sealed the win in the closing moments of the game.
The victory keeps the defending champions level on points with Atletico Madrid at the top of the table.
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