Los Blancos fought back on two occasions, with Vinicius Junior and Lucas Vazquez finding the net to cancel out goals by Andreas Christensen and Fermin Lopez respectively.
The contest appeared to be heading towards a draw until Bellingham arrived at the back post to thump home a stoppage-time winner from Vazquez's low cross.
Bellingham's strike moved Real Madrid to the brink of the league title, with Carlo Ancelotti's side now boasting an 11-point cushion over their Clasico rivals.
Bellingham replicates Ronaldo feat
As well as leading Real Madrid to all three points at the Santiago Bernabeu, Bellingham also became the first Real Madrid player to score in both La Liga Clasicos in the same season since Ronaldo achieved the feat in 2014-15.
Ronaldo found the net in a 3-1 victory in October 2014, before he got on the scoresheet in a 2-1 loss in March 2015.
In contrast to Ronaldo, Bellingham managed to achieve the impressive feat by leading Real Madrid to victory on both occasions.
Bellingham scored a 68-minute equaliser in October's reverse fixture, before he went on to score another stoppage-time winner against Barcelona.
Not only has he matched Ronaldo's achievement, Bellingham has also become the first Real Madrid player since Ruud van Nistelrooy in 2006-07 to score in his first two league Clasicos.
Bellingham in Pichichi race
Having already helped Real Madrid win the Spanish Super Cup, Bellingham will be determined to collect winner's medals in La Liga and the Champions League before the end of the season.
The England international also has the chance to finish his first La Liga campaign as the division's top scorer.
Having scored 17 goals in 25 league matches, Bellingham is currently sitting in second place in the scoring charts and just one goal behind Girona forward Artem Dovbyk.
If he were able to finish the season as La Liga's top scorer, the 22-year-old would become the first Englishman to win the coveted Pichichi trophy.
Bellingham will have the chance to add to his tally when Real Madrid travel to Reale Arena for Friday's clash with Real Sociedad.
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