Los Blancos entered the match level on five UEFA Super Cup trophies with Clasico rivals Barcelona, but the Champions League holders have now moved out on their own due to their two-goal win over Atalanta in Warsaw.
Real Madrid made the breakthrough in the 59th minute, with Federico Valverde turning a low cross from Vinicius Junior into the back of the net from close range.
Rodrygo smashed one against the crossbar late in the first period, before Thibaut Courtois made a wonderful save early in the second half to keep out a header from Mario Pasalic, but Valverde opened the scoring, before Kylian Mbappe registered on his debut in the 68th minute to make it 2-0.
Real Madrid grew into the match after a tight opening 45 minutes, and Carlo Ancelotti's side are already off the mark in terms of trophies for the 2024-25 campaign.
Mbappe scores on first appearance for Real Madrid
Mbappe, as expected, was named in the Real Madrid XI, with the France international making his first appearance for the club, having been given an extended break following Euro 2024.
The 25-year-old started through the middle, with Vinicius to the left, Rodrygo to the right, and Jude Bellingham, who played as a number 10 last term, dropping into a deeper area.
However, Vinicius and Mbappe were swapping throughout the opening half of action.
Mbappe's first big moment came in the 15th minute, when he met a cross from Dani Carvajal, but his strike, which was heading towards the goal at pace, was blocked by a Napoli defender.
The attacker had his moment in the 68th minute, though, brilliantly firing into the back of the net from inside the box to all but secure the trophy for Real Madrid, and it was an encouraging debut for the ex-Monaco youngster.
Real Madrid fans seem to have a new hero in the number nine shirt, and it is difficult to imagine how teams are going to contain the attacking unit of Mbappe, Vinicius, Rodrygo and Bellingham this term.
Man-of-the-Match Bellingham stars in new deeper role
Bellingham scored 23 goals and registered 13 assists in 42 appearances for Real Madrid last season, with the 21-year-old operating as an attacking midfielder behind Vinicius and Rodrygo.
It is incredibly difficult to imagine the Englishman reaching those numbers this term, but he showed that he can play a big role in a deeper midfield position on Wednesday night.
Bellingham was involved in the Valverde goal, finding Vinicius, who delivered into the midfielder, before providing the assist for Mbappe to double Real Madrid's lead.
He was booked in the 35th minute for a foul on Atalanta goalkeeper Juan Musso, but the midfielder curled one just over the crossbar early in the second half and continued to improve as the match progressed.
Bellingham also almost scored with a deflected effort in the 62nd minute, but Musso, who also made an eye-catching save to keep out a Vinicius strike, somehow denied the ex-Birmingham City youngster.
What is next for Real Madrid and Atalanta?
Real Madrid will now switch their attention to La Liga, with their opening match of the new campaign taking place against Mallorca on Sunday evening; Eduardo Camavinga and David Alaba will be their only two absentees for that match as it stands, with the team not suffering any fitness problems in the UEFA Super Cup.
Ancelotti's side took a while to warm up on Tuesday, but they have the look of a team that will take some stopping in both La Liga and the Champions League again this term.
Atalanta, meanwhile, will open their 2024-25 Serie A campaign against Lecce on Monday night, and Gian Piero Gasperini's side will be bidding to finish in the top four once again, having claimed fourth last term.