The Blues will pay an initial £72m ($95m) to bring the 21-year-old to Stamford Bridge, with the remainder of the fee to made up in installments
Havertz has long had an agreement in place with the Bundesliga club that he can move away for their asking price as he targets the next step in his career.
Leverkusen wanted the money upfront, but with their star man pushing for the move, they seem willing to relent on small details to complete his departure.
The west Londoners had to ultimately offer more than their last bid, which fell (£18m ($24m) short for the soon-to-be most expensive German transfer of all time.
Havertz's imminent arrival marks a further statement of intent from Chelsea following the signings of Ajax playmaker Hakim Ziyech and RB Leipzig striker Timo Werner for a combined cost of £91m ($114m) earlier this year.
Meanwhile, Frank Lampard is also being backed in his bid to bolster his defence, with his primary target - Leicester City's Ben Chilwell - closing in on move that is expected to be worth around £50m ($65m).
The 23-year-old England left-back is currently in London having further tests on an injured heel, though deal is expected to be concluded soon regardless of the severity of the issue.
Alongside that, the Blues have offered Paris Saint-Germain central defender Thiago Silva a one-year contract with an option included to extend it for further 12 months.
The defender, who will turn 36 in less than a month, has already announced his exit from Parc des Princes.
“It was my last game for Paris,” he told RMC Sport following Sunday's Champions League final. “I am sad. I apologise to the fans. I thank all the supporters for their love. I'll come back with another role in this club I loved. I want to play for another 3-4 years and play in the World Cup in Qatar.”
The arrival of the veteran on a free transfer is a sign the Blues are coming close to their limits in terms of transfer spending having not yet offloaded any players for serious money this summer.
Chelsea are planning more outgoings, with Michy Batshuayi having drawn interest from Leeds United among many other clubs.
The Blues are cautious about accepting, and are attempting to insert an obligation to buy clause at around €22m (£20m/$25m) to recoup some of the £40m ($52.5m) they paid to sign him from Monaco.
Elsewhere, Inter have not yet pushed forward with their interest for Emerson Palmieri, but the Blues are willing to negotiate for a €28m (£25m/$32m) deal as Chilwell prepares to arrive.
Further targets include West Ham's Declan Rice and Brighton's Ben White in defence, while Atletico Madrid's Jan Oblak and Ajax's Andre Onana are options in goal.
Moves for such players could lead to the permanent exit from the club of one of Chelsea's centre backs and goalkeeper Kepa after the Blues conceded 79 goals in all competitions last season.
Chelsea have also signed free agent Xavier Mbuyamba after his release from Barcelona, but the 18-year-old defender will initially link up with the academy set-up at Cobham.