Trailing 1-0, Barca fought back late on to win 2-1 thanks to goals from Messi and Luis Suarez.
Diario Gol says the move was made after Valverde spoke with a furious Messi at halftime. The Argentine was seen complaining and gesturing to Semedo and Digne during the first-half as Barca struggled to find a way past the Alaves rearguard.
The introductions of Alba and Roberto changed things for the better, with both players close to Messi.
The victory left Real Madrid 19 points behind LaLiga leaders Barca.