"Obviously it's a great result for us, but you don't want your national team colleagues to experience something like that," Neuer said as Barcelona suffered their heaviest defeat in Europe.
Thomas Mueller and substitute Philippe Coutinho both scored twice for Bayern alongside Ivan Perisic, Serge Gnabry, Joshua Kimmich, Robert Lewandowski who also netted.
Barcelona had only a David Alaba own goal to show before Luis Suarez offered brief hope with a second-half goal.
The quarter-final in Lisbon had been a chance for Ter Stegen, 28, to advance his claim to take over from Neuer, 34, as Germany's goalkeeper.
The pair had a war-of-words last September as the Barcelona goalkeeper questioned why Neuer remains first choice under national team head coach Joachim Loew.
However, Neuer comfortably won Friday's dual, wrong-footed only by Alaba's mistimed clearance and Suarez's strike.
Neuer can expect to be in Germany's goal for their Nations League matches against Spain and Switzerland early in September.
"We are of course very euphoric. This is something very special," said Germany team-mate and Bayern midfielder Leon Goretzka.
"It will probably only sink in during the coming days."