Luis Suarez followed his midweek brace in the 3-1 UEFA Champions League triumph at Paris Saint-Germain with a first-minute opener at the Camp Nou on Saturday.
But the league leaders turned in a laboured first half display as Valencia captain Dani Parejo had a penalty saved and Andre Gomes hit the post for the visitors.
Lionel Messi sealed the points deep into stoppage-time with his 400th Barcelona goal but afterwards Luis Enrique suggested his players were "empty" after their exertions this week.
"It was a great start to the game with that goal in the first minute, but from there we had problems," he told a press conference.
"We committed uncharacteristic errors, we had more problems than usual to approach the opposition goal.
"They had a lot of chances and they deserved better.
"After the break we made some changes and we played the game we wanted to do.
"This is a great result. We must congratulate the players because they are empty."
