Goals from Marouane Fellaini, Marcus Rashford and Romelu Lukaku help United ease to victory but that didn't dampen the party atmosphere in the stands.
Fans of the Swiss champions were seen setting off flares pre-match leaving the club now facing sanctions.
UEFA's control, ethics and disciplinary body will deal with the case on October 19th, with Basel likely to face a fine.
French side Saint-Étienne were hit with a £45,000 fine after their fans committed a similar offence at Old Trafford before a Europe League tie in March.