The Bundesliga leaders were beaten 2-0 by Arsenal in Germany on Wednesday, but progressed on away goals after the Gunners had levelled the aggregate score to 3-3.
It will be the first time since the 1995-96 season that no clubs from England turn out in the quarter-finals, and Heynckes says that Premier League is not as strong as it is often portrayed.
"The gap between the Bundesliga and the Premier League is not as big as it has been made out," Heynckes told ESPN.
"The English teams had an unlucky draw, with Manchester United against Real Madrid and Arsenal with us. Arsenal will be back again."
Manchester United, Chelsea and Manchester City had all been dumped out of the competition prior to Arsenal's exit.