The mercurial Argentine thought that he had given the Catalan giants the lead in a top-of-the-table encounter at the Mestalla.
With 30 minutes on the clock, Messi saw Valencia goalkeeper Neto fumble an effort from the edge of the area, resulting in the ball clearly crossing the line.
Neither the referee nor his assistant awarded a goal, however, and with there no goal-line technology or VAR on offer in La Liga, Barcelona and their talismanic forward were left frustrated.
Alba, who snatched a late leveller in a 1-1, told reporters on the incident after the final whistle: "It was a mistake by the referee.
“Even from the middle of the pitch I could see it.
"At the break we saw the replay and it is clear, these plays can't be missed."
Alba struck eight minutes from time to earn Barca a point in a crunch clash, with his strike cancelling out an opener from Rodrigo on the hour mark.
The result leaves Ernesto Valverde’s side four points clear of Valencia at the La Liga summit, with Los Che continuing to show that they are genuine contenders for the crown.
Alba added on his former club: "The league table shows it, they are a clear candidate.
”There is a lot of football left to play.
"However, they are second for a reason."
It is, however, the Messi incident which will dominate the headlines for now.
Valverde told reporters after the game: "We were in total control in the first half and we had a goal cancelled. In the second half, Valencia decided to pressure us and move forward more. Their goal hurt us, so we moved forward to attack more.
"The cancelled goal damaged us and it was the wrong decision by the assistant referee."
Having seen a perfectly good effort ruled out, Messi is now on his worst scoring run in seven years – with six games having come and gone without finding the back of the net.