The Argentine forward's shot in the 30th minute was fumbled by Neto and the ball crossed the line before the Valencia goalkeeper hooked it back and the game continued.
Referee Ignacio Iglesias Villanueva and his assistants did not award the goal and Valencia played on while Barcelona players celebrated the goal which would have put them 1-0 up.
'Scandal', read the front page of Mundo Deportivo on Monday, while Sport said it was "a refereeing robbery".
La Liga is the only one of the big five European leagues that does not yet use either video or goalline technology to help get the key decisions right.
Madrid's newspapers Marca and AS both acknowledged the controversy and that the result means the race for La Liga is still on.
The draw leaves Barcelona four points clear of Valencia and eight ahead of both Atletico Madrid and Real Madrid.
Marca journalist Diego Pico wrote: "A huge mistake from the refereeing team which unleashes an old controversy. Technology is more than necessary, especially for goals like this which aren't even 'ghost goals'."
La Liga president Javier Tebas said earlier in November that the VAR (Video Assistant Referee) system would be introduced next season.
"Next season there will be VAR in La Liga, without a doubt," Tebas said.
"We are making lots of progress in meetings about it right now and it will be ready very soon."
However that is too late for Barcelona, who suffered an identical problem earlier this year, in a 1-1 draw with Real Betis in January.
On that occasion, Jordi Alba's shot crossed the line as Betis defender Aissa Mandi tried to clear it but referee Alejandro Jose Hernandez Hernandez did not award it.
Barcelona finished three points behind Real Madrid in the 2016-17 season and that goal could have affected the outcome of the title race.
"There will be a lot of things that VAR can't clear up, but I hope that they can help with things likes today," Barcelona midfielder Sergio Busquets said.
"It's an evolution which we need. It's something we need."
