The prolific forward netted twice to lead Bayern to a 4-1 victory over his former club but he was forced off in the second half after suffering a shoulder injury following a foul from goalkeeper Roman Burki, having previously been the victim of a strong challenge from Marc Bartra.
"I got the feeling that Dortmund wanted to eliminate Robert at all costs," Barthel told Bild.
Dortmund sporting director Michael Zorc, however, has laughed off such claims and was quick to stress there was no foul play on show in Der Klassiker.
"This is absolute nonsense," Zorc insisted.
"Of course, it was a foul from Burki, but we always tried to keep Robert out of the game in a fair way."