The Blaugrana went behind from a Manuel Iturra strike but scored twice in two minutes to take the lead - Lionel Messi capitalising on a defensive error before Carles Puyol nodded in from a corner.
However, Ignacio Camacho’s strike in the 89th minute ensured the quarter-final match with Manuel Pellegrini's men ended all square, but Vilanova believes that the late goal does not change anything heading into the second leg in six days' time.
"There was a big difference between the first and second half. During the first, we played at a very high level, but we could not finish the tie," he told reporters after the game.
"For us, nothing changes. We always go out to win the game, so we will do that in Malaga too."
Thiago’s mistake in the first 45 allowed Iturra to score and although Alexis Sanchez lacked an attacking threat on Wednesday night, Vilanova defended his players insisting errors are part of the game.
"Mistakes always happen in football," the head coach added. "Thiago gave us an example of how difficult it is to get the ball played from behind. He [Thiago] risked a lot and this can happen.
"With Alexis, the thing to do is to try to help. He's a young player and has all the talent in the world.
"We must protect him, and to help him do all that is possible within football. Football has already swallowed hundreds of players and we have to take care of our own."