Heynckes is back in charge of the Bavarians after Carlo Ancelotti was sacked following a poor start to the season.
The 72-year-old enjoyed a break from the game after leaving Bayern in 2013, but insists the club now need to spend big to capture the best youngsters in Germany.
Werner joined RB Leipzig in 2016 for 10million euros after former club Stuttgart were relegated and Heynckes insists it was a missed opportunity by the German giants.
"A club like Bayern should have signed a Timo Werner from Stuttgart years ago," he told ESPN. "The best players must play - it does not matter whether they are old or young.
"Do you think that a Franck Ribery can always expect to play? No. When he is not on form, he will not play.
"As I said, you have to look after good, young players in a timely fashion. You have to challenge, speak, lead and motivate them."