A point maintains Barca's four-point lead over Valencia at the top of La Liga, but the Catalans were forced to do it the hard way after Messi's 30th minute strike that slipped through Valencia 'keeper Neto's legs was somehow not seen to have crossed the line by the officials.
Unlike in Europe's other top leagues, La Liga has so far refused to introduce goal line technology due to cost concerns.
"Messi's goal was very clear," said Valverde. "The important thing is to not let the tension of the game overcome you and we didn't lose our concentration against a very strong opponent."
"It was a good game, a little marred by one controversial moment."
"We know the potential Valencia have at home and although we don't go away completely satisfied, we managed to take something positive from the game."
After a first-half performance well below the form they have shown so far this season, Valencia improved markedly after half-time and went in front when Rodrigo tapped home from close range.
However, Barca responded to protect their unbeaten record in La Liga this season when Messi's splendid pass was volleyed home by former Valencia left-back Jordi Alba eight minutes from time.
"It was a monumental error by the referee," blasted Alba to Movistar.
"Even I could see it was in from the middle of the pitch. We saw the replay at half-time and it's clear."
La Liga intends to introduce video assistant refereeing (VAR) for controversial decisions next season.
However, Barca midfielder Sergio Busquets believes that is too late for a league that likes to market itself as the best in the world thanks to the presence of Messi and Real Madrid's Cristiano Ronaldo.
"La Liga has the best players in the world and the best league also deserves the best technology," said Busquets.
A share of the spoils allows Real Madrid and Atletico Madrid to close back to within eight points of Barca at the top of the table.
Yet, Alba believes Valencia's stunning start to the season means they deserve to be treated as title contenders.
"I played here for many years and it is always difficult to win here," added the Spanish international.
"They are clear candidates. There is a long way to go, but they are well organised and know what they want to do."
Valencia boss Marcelino Garcia Toral, who has rejuvenated Los Che after two seasons in the doldrums, was forced to watch from the stands as he served a touchline ban.
Assistant coach Ruben Uria admitted the hosts had been handed a huge slice of luck and also backed the introduction of technology as soon as possible.
"It is a shame that these situations still arise."
"We are in favour of technology and this time it has fallen in our favour."