Napoli had little time to recover before FC Barcelona doubled their lead.
Referee Paul Tierney missed the initial incident, but after consulting the VAR screen, he awarded United a penalty, which Bruno Fernandes duly converted.
But Guardiola yelled from the sidelines for the 22-year-old Haaland to take the penalty kick they had been awarded in the closing minutes.
Manchester City will go into next week’s clash with Liverpool with a one-point lead.
Today’s defeat comes after the gunners were trashed in their first and second game by newly promoted Brentford and Chelsea.