The Basque outfit were 2-0 down to goals from Pedro and Leo Messi but Barcelona had Gerard Pique sent off.
That allowed the home team to fight their way back, winning late on thanks to a goal from Imanol Agirretxe in stoppage time.
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The reputation of the Premier League means it is the most popular and one of the most watched leagues in the world.
Five English clubs will compete in the last sixteen of the Champions League for the first time ever as Liverpool, Manchester United, Manchester City, Chelsea and Tottenham face some difficult away matches.