Los Blancos found themselves 2-0 down to Almeria at the Bernabeu going into the break following goals from Largie Ramazani and Edgar Gonzalez.
But Carlo Ancelotti's men came back to land all three points with a Dani Carvajal winner in the ninth minute of stoppage time - though there was plenty of controversial moments in between.
Bellingham scored a penalty to start the comeback, but before he got on the score sheet, a flashpoint with the match official was caught on camera.
After referee Francisco Jose Hernandez Maeso blew up for half-time and boos rang around the Bernabeu, Bellingham made a beeline for the official.
The England international was furious after he failed to win his side a free-kick, as he exclaimed: "That's a foul on me there!"
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The referee admitted his mistake, saying: "I agree with you on that one."
That saw Bellingham blow his cool, turning around and storming off as he said: "Oh my God… brilliant.
"I don't get a f****** foul for you agreeing with me though. It's just f****** s*** man, every week. F****** hell."
While the 20-year-old fumed over decisions going against him, Real Madrid certainly benefited from some iffy VAR calls after the break.
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The first came when VAR intervened and suggested a penalty be given for handball, which Bellingham duly converted.
An argument could be made that the Almeria defender was pushed, but the ball certainly struck his arm.
Another VAR decision went Madrid's way when Sergio Arribas scored against his former club before the goal was ruled out for a foul in the build-up from Dion Lopy.
The midfielder was adjudged to have fouled Bellingham after nipping in and getting the ball as a flailing arm brushed the former Borussia Dortmund star's face.
The third incident saw Vinicius Jr score to make it 2-2 only for the referee to disallow it for handball.
However, VAR intervened yet again to inform the on-field official to reverse his decision, though replays showed that the original decision might have been correct.
In the end, Real took all three points with a last-gasp goal from Carvajal, taking advantage of the added time due to all the VAR stoppages to break Almeria hearts.
It keeps Los Blancos a point behind league leaders Girona, who are this season's surprise package with Barcelona eight points off the top.