The fullback insists his celebration was meant to hail the Argentine's brilliance and not to provoke the home supporters.
The 23-year-old's actions in the aftermath of the strike have come under scrutiny following a game already marred by the dismissal of Victor Valdes after the full-time whistle, but he was quick to defend his conduct.
"I used my index finger to show that Messi is the best in the world, and that he deserves the praise," Alba insisted to reporters. "My gesture to the fans wasn't bad.
"A draw would have been the fairest result, but we need to leave this behind and focus on the matches against Deportivo and AC Milan.
"We left without any points, but know we still have a good advantage over Atletico and Real Madrid. We have to give it our all and even more so against Milan. We have confidence in ourselves."
Gerard Pique also revealed his disappointment and called for the team to improve significantly after suffering a second Clasico defeat in the space of a week.
"When you come to the Bernabeu, you have to be very superior to Madrid in order to win," the Spain international lamented. "We have to give a lot more of ourselves. We weren't fluid like we usually are and we’re missing certain things. While we've had these bad moments when we won plenty of titles, we still have to end this poor streak as soon as possible.
"I don’t think it’s the right moment to criticize our style of play though, we've secured a lot of good results with it. We have the right team to get out of this situation. We’re confident that we’ll eliminate Milan, but first we have to defeat Deportivo."