Werner will team up with the Premier League giants on 1 July after Frank Lampard's side activated his £47.5-million release clause to lure him away from the Bundesliga.
The 24-year-old had the chance to remain at Leipzig to complete their league campaign and Champions League season after helping them qualify for the quarter-final stage of the competition.
However, he's now sought to explain why he's leaving prematurely to depart for London after becoming the club's all-time record goalscorer by netting his 94th goal in his final game.
"Of course it hurts me that I can't help out [RB Leipzig] to play in the Champions League. But I'm a Chelsea FC player from July 1st and I'm being paid by Chelsea from then on, Werner told Sportbuzzer.
"It was clear that all parties - Chelsea, RB and my side - should and must settle this. Of course, I tried to keep out of the Champions League issue as much as I could because it was clear that I would have to hurt one side. That's why my agent finally agreed it with the clubs."
The 29-time capped Germany star has scored 34 goals and registered 13 assists in 45 games across all competitions for Die Bullen this season.