The pair combined perfectly with Tel whipping a cross into the box and Choupo-Moting drilling in to give Bayern the lead in the ninth minute.
Israeli keeper Daniel Peretz made his Bayern debut in goal but was rarely troubled in a one-sided encounter which was briefly interrupted after 30 minutes.
Bayern fans threw hundreds of tennis balls onto the pitch, in protest against the decision to hold the German Super Cup last month on the day of the Cup first round, forcing Bayern to delay their first round match.
It had no effect on their team's performance as they struck twice more in the first half to put the game to bed.
France youth international Tel added a fourth from a tight angle in the 85th to continue his good form, having also scored three goals in the league so far this season.