Werner leaves Chelsea after just two seasons in West London.
The 26-year-old joined Chelsea from Leipzig for £45m in the summer of 2020 and won the UEFA Champions League in his first season at the club.
He added the UEFA Super Cup and FIFA Club World Cup to his list of laurels the following season but his time at Chelsea was largely underwhelming as he could not recapture the form that made him such a hot cake in Germany.
Werner only scored 10 Premier League goals in 56 appearances for Chelsea, with 23 strikes arriving from 89 appearances across all competitions.
The Germany international scored a club-record 95 goals in 159 games for Leipzig in his first spell at the club between 2016 and 2020.
Werner has signed a four-year contract with Leizig, who have parted with £25m for his services.
In a parting message to Chelsea fans, Werner wrote: 'Dear Blues, Today marks the end of my journey with Chelsea FC.'
'I am incredibly grateful for the time I spent at this special club.
'At this point I would like to express my appreciation for my teammates, the coaches staff, and especially for you, the special supporters of Chelsea Football Club.
'I felt so much love and support throughout the last two years and I will never forget how you guys stood behind me in good and challenging times!
'We lifted trophies like the Champions League together and I will always remember the song you wrote and chanted for me. I'm already looking forward to hopefully playing at Stamford Bridge again one day!
'See you soon, Timo.'
On his return to the Red Bull Arena, Werner added: "I'm very happy to be playing for RB Leipzig again from now on."
"It was a great time from 2016 to 2020 in which we caused a sensation as a league newcomer. It was a worthy farewell for me back then, going as a record goalscorer.
"But that's also a bit of the past and now I'm looking ahead, because RB Leipzig has developed over the past two years, just like I have."
