The 24-year-old defender made the switch to Leverkusen from fellow Bundesliga outfit Freiburg in 2011, and has become a mainstay of the first team.
Toprak's deal was initially due to come to an end in June 2016, but that has now been extended for a further two years.
And the centre-back is thrilled to extend his stay with coach Sami Hyypia's charges.
"I am delighted to have signed this deal," he told the club's official website. "We have a strong side who can achieve their ambitions – that's why signing the contract was such an easy decision."
Leverkusen sporting director Rudi Voller added: "Omer made huge strides last season. He is now taking greater responsibility on the pitch and has became dangerous in front of goal.
"We see him as one of the cornerstones of our team. He will get even better over the next few years – that's why it was so important to get the deal done."
