Hegeler, who turns 25 on Friday, came through the youth ranks with the club and has shown his commitment by penning a new deal.
"We are delighted to have been able to tie Jens down to us in the long term," said Leverkusen's general manager Wolfgang Holzhauser.
"He has proven his high value to the team in recent months and is far from reaching the end of his development."
Hegeler says he identifies with the club's philosophy and can see a bright future in Leverkusen.
"We have a young team which is hungry for success and the club is aiming to establish itself at the top end of the Bundesliga, setting targets in Europe and we've been working for years on the future," he said.
"I therefore think there is still a lot we can achieve and I am really looking forward to being successful with Bayer."
Leverkusen currently trail second-placed Borussia Dortmund by four points, yet they have a six-point advantage over Eintracht Frankfurt in fourth and are on course for a place in the Champions League next season.