The coach was left to rue his side's performance after the break as the reigning Spanish champions ended a 25-match league winning streak at Camp Nou.
The defeat ended a run of 25 straight league victories at Camp Nou, stretching back to round seven of the 2012-13 season when Barca was held to a 2-2 draw by Real Madrid.
The reigning Spanish champions went into the halftime break at 1-1 after Daniel Parejo had equalized Alexis Sanchez’s opener but second-half goals from Pablo Piatti and Paco Alcacer - either side of a Lionel Messi strike - gave Los Che a famous victory.
"After the first 30 minutes, I can’t explain how the game changed after that. We were a different team in the second half,” Martino told a press conference.
"Before the game I said that one pays dearly for every mistake from now on and we made several today.
"When you have the chance to finish off your opponent, you must do it. You shouldn't give them chances to come back. Today we did that and Valencia took advantage."
The defeat means second-placed Atletico Madrid will have the chance to go three points clear at La Liga’s summit when it hosts Real Sociedad on Sunday, while Real Madrid can leapfrog Barca with a win at Athletic Bilbao.