After losing 3-2 at home to Zenit St Petersburg in their opening game, Valencia revived their bid for a place in the round of 16 when a Sofiane Feghouli effort secured a 1-0 success in Lyon last month.
The Algeria international was again decisive at a rainy Mestalla, vying with Nielsen to be first to a Joao Cancelo centre and forcing the Dane to put the ball into his own net in the 15th minute.
Valencia almost doubled their lead 10 minutes later but Santi Mina and Dani Parejo were denied by a superb double save from goalkeeper Matz Sels.
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The visitors levelled five minutes before the break when Thomas Foket chested the ball down in the penalty area and smashed a superb angled shot high past Jaume Domenech in the home goal.
Valencia struggled to exert control in the second half, with the fans at the Mestalla becoming increasingly frustrated until a Jose Gaya cross-shot ricocheted into the net off the unfortunate Mitrovic 18 minutes from time.
It was hardly a vintage performance from Valencia, back in the Champions League after a two-year absence, but tightened their grip on second place in the section with six points.
Zenit lead on a maximum nine points after they won 3-1 at home to Lyon, with Ghent and Lyon each on one point.
(Writing by Iain Rogers, editing by Pritha Sarkar)
