The England midfielder, making his return from injury, thought he had headed home a cross deep into stoppage time at the Mestalla but the referee had already blown for full time.
Real players surrounded the official in a chaotic aftermath and Bellingham was shown the red card before the players left the field.
It made for a dramatic ending to a compelling LaLiga clash in which the leaders had fought back from 2-0 down with two Vinicius Junior goals.
Valencia had stunned Carlo Ancelotti’s side by pouncing on two mistakes to score twice in quick succession through Hugo Duro and Roman Yaremchuk.
The result meant Real missed the chance to move nine points clear at the top and second-placed Girona will have the chance to cut the gap when they play Mallorca on Sunday.
It was an emotional night for Valencia, who were returning to action for the first time since a deadly fire in their city, with tributes paid to victims and other people affected before kick-off.
The game got off to a slow start as the visitors struggled to create any meaningful opportunities despite dominating possession.
It was not until the 23rd minute that Real caused any alarm in the Valencia box as Vinicius, returning to a ground where he was racially abused last season, went down under a challenge from Dimitri Foulquier. No penalty was given.
Valencia took the lead against the run of play in the 27th minute after Real lost possession.
There was an element of fortune about it as Foulquier crossed to the far post and Fran Perez miskicked his attempt to clip back across goal. Duro, who had not been expecting the ball, reacted quickly to head home.
Dani Carvajal then compounded the setback moments later with an underhit backpass that Yaremchuk seized upon to round Andriy Lunin and slot in.
Real recovered and Bellingham, back in the side after three weeks out, created a chance for Federico Valverde but Giorgi Mamardashvili was equal to his effort.
The pressure paid off in first-half stoppage time as a Carvajal cross took deflections off a defender and Mamardashvili and found its way to Vinicius for a simple tap-in.
Real upped the tempo after the break and Vinicius lashed a shot wide before Bellingham, who has enjoyed a stunning first season at the Spanish giants, wrong-footed the defence and forced Mamardashvili to save with his legs.
Diego Lopez brought a good save from Lunin at the other end but further Real pressure paid off when Vinicius rose to head in a Brahim Diaz cross.
There was a long delay late on after Valencia’s Mouctar Diakhaby suffered a serious-looking injury and was carried off on a stretcher.
Real had a scare in stoppage time when Valencia were awarded a penalty for a foul on Duro by Nacho but the decision was overturned by VAR.
It was not the end of the drama but Bellingham’s effort came too late to count.