An opening goal by Vinicius Junior, followed by a moment of Jude Bellingham brilliance and a Federico Valverde long-range effort, kept Madrid's perfect record in the competition intact.
Napoli fought hard to secure a 2-1 win over Braga in their first Champions League outing of the season and were bidding to earn their first win over Real Madrid in four previous meetings in this competition, but it was not to be.
After sneaking a last-gasp win over Union Berlin in week one of this year's Champions League group stages, Carlo Ancelotti returned to the stadium where he was manager until 2019, this time in the opposing dugout.
The opening quarter of an hour was fairly even, with both sides creating a few half chances, but it was the hosts that drew first blood after Natan's header from Piotr Zielinski's left-sided corner hit the crossbar, but Leo Skiri Ostigard seized the rebound, overpowering two Madrid defenders to open the scoring.
However, The Blues' lead was short-lived as the visitors struck back within eight minutes of going behind when Bellingham surged into the penalty area to set up Vinicius, who slotted his shot cooly past Alex Meret.
While Bellingham was not brought to Madrid specifically to replace the departed Karim Benzema, that is exactly what the 20-year-old seems to be doing as he got his eighth goal in nine matches for Los Blancos with a superb solo run 10 minutes before the break.
The England international, who also scored against Scotland during the international break, picked up the ball near the halfway line and strode into the box, taking four opponents with him, before finishing in the bottom-right corner.
That goal also earned the former Borussia Dortmund man a piece of club history as he became only the third Madrid player to score in his first two Champions League matches, following Christian Karembeu in the late 1990s and Cristiano Ronaldo back in 2009.
Despite Los Blancos heading down the tunnel at half time in the lead, there was an evident feeling that we had not seen the last goal of the match.
That feeling was turned into reality less than 10 minutes after the restart, with VAR sending Clement Turpin to the monitor just nine minutes after the restart, and after a thorough examination, the referee awarded Napoli a penalty, which Zielinski stepped up and smashed off the inside of the woodwork to pull The Parthenopeans level.
Ancelotti and his players were in clear disbelief with the decision by the referee and could perhaps be excused for their reactions as it was a call that could genuinely have gone either way.
However, while still feeling a little hard done by, Los Blancos responded excellently as a Luca Modric corner was cleared only as far as Valverde, who fired an absolute thunderbolt at goal, and while Meret got a touch on it, he was unable to keep it from crashing off the crossbar and into the net.
The visitors saw out the match well from there on and will need to reset quickly for their encounter against Osasuna this weekend, while Napoli have a tricky fixture at home to Fiorentina.