Both German teams topped their groups, with BVB impressively finishing above respective league winners Real Madrid, Manchester City and Ajax.
But Hitzfeld, who has coached both Bundesliga clubs, doubts Schalke will win the European trophy due to lack of consistency.
“I do not see Schalke [winning the trophy] as they never have the necessary consistency,” he told Bild. “But I think both Dortmund and Bayern could win the Champions League.
"The fact is, the German league is as strong as ever."
The current Switzerland boss also ruled out a return to the Bundesliga in the near future, and hopes to guide Switzerland to the 2014 World Cup.
"I cannot imagine returning any time soon,” he added. “I have a contract until 2014 in Switzerland and would like to go the World Cup in Brazil.”