The Premier League side confirmed Werner will join the club in July following the completion of the Bundesliga season, subject to passing a medical which has been delayed as a result of the coronavirus pandemic.
"I am delighted to be signing for Chelsea; it is a very proud moment for me to be joining this great club," Werner said. "I of course want to thank RB Leipzig, the club and the fans, for four fantastic years.
"You will forever be in my heart. I look forward to next season with my new teammates, my new manager and of course the Chelsea fans. Together we have a very successful future ahead of us."
Werner's desire to begin life in west London has been key to the timing of the agreement. Leipzig's final Bundesliga match takes place at Augsburg on June 27, but their season will not end until August due to the rescheduling of the Champions League latter stages.
However, the 24-year-old informed Leipzig that he wished to join Chelsea as soon as possible rather than wait to complete the European campaign because of the issues that could cause at the start of his career at Stamford Bridge.
The Champions League final is scheduled for Aug. 23 and with the 2020-21 Premier League season expected to begin in mid-September, Werner could have faced a truncated start to the new campaign.
He is yet to undergo a medical due to travel restrictions resulting from COVID-19. Werner cannot travel to London while the Bundesliga season is ongoing while Chelsea's doctors have opted not to fly to Germany because of United Kingdom regulations demanding anyone arriving back in the country from abroad must immediately self-isolate for 14 days, but no issues are anticipated
"We are very excited that Timo Werner has chosen to join Chelsea. He is a player who was coveted all over Europe and it is no surprise, he has that rare mix of being young and exciting and yet established and proven," Chelsea director Marina Granovskaia said.
"We can't wait to have Timo on board, but until then we wish him and RB Leipzig all the best for the rest of this season."
Werner decided to join Chelsea after Liverpool opted not to make a move for the Germany international despite Reds boss Jurgen Klopp being a long-standing admirer.
He has scored 32 goals and set up a further 13 in 43 appearances for Leipzig this season in all competitions and becomes the club's second summer signing after the £38m capture of Hakim Ziyech from Ajax.