The home side continued their good start and Visca scored the second from another perfect counter attack play.
French forward Antony Martial hit back immediately after the restart to reduce the deficit, before the end of the first half.
Manchester United failed to find the much needed equaliser in the second half and Istanbul Basaksehir held on for their first victory in the competition.
Meanwhile, Nigeria international Azubuike Okechukwu who plays for Istanbul Basaksehir also missed the game as he continues to work to regain full fitness.
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