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.
The Turkey international is part of a side that has reached the UEFA Champions League round of 16, after qualifying as runners-up from Group A.
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."
Leverkusen sit second in the Bundesliga, having taken 37 points from 17 matches, and will battle Paris Saint-Germain for a spot in the quarter-finals of the Champions League.
