Los Blancos missed the chance to open up an eight-point lead at the top of the table at Mestalla, where Hugo Duro and Roman Yaremchuk propelled the hosts into a surprise two-goal lead.
Vinicius Junior managed to cut the deficit in half just before the break, though, and the Brazilian notched his second of the afternoon in the 76th minute to get the La Liga leaders back on level terms.
From two goals down, Carlo Ancelotti's men thought that they had completed an exceptional turnaround deep into second-half injury time, when Bellingham headed in from Brahim Diaz's cross.
However, the whistle had blown just before Diaz sent his delivery into the box, and an unmoved Manzano was quickly surrounded by furious Real players, who had to be calmed down by Ancelotti.
Bellingham was sent off in the furore, and in their official match report, Real Madrid described Manzano's decision as "unprecedented" as their title aspirations suffered a marginal dent.
"An unprecedented refereeing decision by Gil Manzano prevented Real Madrid from beating Valencia at Mestalla," Real Madrid wrote. "With the score at 2-2 and in the last play of the game, Brahim crossed into the box and Bellingham headed home to make it 3-2.
"But the referee disallowed the goal as he had blown for full-time when the Malagueño's pass was still in the air. The LaLiga leaders deserved all three points, but had to settle for a point after coming back from 2-0 down. Two goals from Vini Jr. tied the match, which was finally settled by Gil Manzano's decision."
Ancelotti echoed Real Madrid's sentiment in his post-match press conference and also claimed that Bellingham did not insult referee Manzano, only using profanity to the official while remonstrating at the end.
"There's not much to say. Something unprecedented has happened and it's never happened to me before. After the rebound we had possession. It's never happened to me before and there's nothing more to add," Ancelotti said.
"We were annoyed by Bellingham's red card because he didn't say anything insulting. It was frustration. He said: "it's a fucking goal" and that's the truth. The player was clear in what he said.
"It's true that he came on vehemently after the goal and that's normal. It was not an insult at all. Let's see what the referee writes in the official report. We are upset and angry. It's normal but we have to get back to normal because we have an important game on Wednesday.
"In the game there were good things and things we have to improve upon. We have to cool down a bit because the team is still seething. To cool down you have to look at the table. We can still sleep well tonight."
Despite falling victim to a bizarre call at Mestalla, Real still boast an insurmountable six-point lead over Girona at the La Liga summit and now turn their attention to Wednesday's Champions League last-16 second leg with RB Leipzig.
Los Blancos ran out 1-0 winners over the Bundesliga outfit at the Red Bull Arena thanks to a stunning effort from Diaz in place of injured Bellingham, who will be fine to face Leipzig despite his domestic sending-off.