Messi's tame shot in the 30th minute was spilt by Valencia goalkeeper Neto and bounced over the line before the Brazilian dragged it back over.
Messi celebrated along with his team mates but referee Ignacio Iglesias Villanueva allowed play to continue and Valencia almost scored at the other end as Simone Zaza flashed a shot just wide, narrowly averting more controversy.
Valencia took the lead on the hour with a close-range strike from Spain international Rodrigo Moreno which looked set to reduce Barca's advantage at the top to a point.
But Alba met a gorgeous lofted pass from Lionel Messi to equalise in the 82nd minute, denying his former side their first home win over Barca since 2007.
The Catalans lead the standings on 35 points after 13 games, while Valencia have 31. Atletico Madrid and champions Real Madrid are third and fourth respectively on 27.
"In the end, the important thing is that we scored the goal but the referee made a monumental error, even I saw it from the middle of the pitch," Barca defender Jordi Alba told reporters.
"We watched it at halftime and it was clear. It was very clear. You can interpret a foul in a certain way but plays like this have to be seen."
TEAMS FRUSTRATED
Spain’s top flight is the only one of Europe’s leading five leagues which has so far shunned the use of goal-line technology, much to the frustration of the teams.
Last season Barca were not awarded a goal despite television replays showing the ball had crossed the line during a 1-1 draw with Real Betis.
The Spanish soccer federation (RFEF) announced this month that the Video Assistant Referee (VAR) system would used in the league from the start of next season, joining Germany's Bundesliga and Italy's Serie A who are using the technology.
VAR involves assistant referees watching the action remotely and then drawing the match referee’s attention to officiating mistakes or serious incidents that have been missed.
While goal-line technology just determines whether the ball has crossed the line, VAR can also be used for decisions on red cards, penalties and cases of mistaken identity.
"There will be a lot of things that VARs can’t clear up, but I hope that they can help with things likes today," Barca midfielder Sergio Busquets said.
"It’s an evolution which we need. It’s something we need. And not just for this goal.
"La Liga has the best players in the world, it’s the best league in the world and it deserves the best technology. The goal was over the line, but neither the referee nor the assistant saw it," he added.
(Reporting by Richard Martin; Editing by Ken Ferris)
