Werner went down with an ankle injury moments after laying on the assist for the first goal in RB Leipzig's 4-0 UEFA Champions League win over Shakhtar Donetsk on Wednesday.
The 26-year-old has found some much needed for since rejoining Leipzig from Chelsea this summer.
Werner has scored nine goals and provided four assists in 16 appearances across all competitions for Marco Rose's men.
The former Stuttgart forward was set to be a part of Germany manager Hansi Flick's 26-man squad for the tournament which kicks off in three weeks time.
Leipzig provided an update on Werner's injury on Thursday, revealing that he will miss the rest of 2022 in order to make a full recovery.
"Timo Werner suffered an ankle injury last night in the win over Shakhtar Donetsk," read a club statement.
"Scans today in Leipzig showed that he has unfortunately torn the syndesmosis ligament in his left ankle and will therefore be out for the rest of 2022."
Werner himself added an update on social media, posting on Twitter: " A very tough one to take for me! I will be out for the next weeks, will miss the World Cup and will have to support RB Leipzig and Germany from the couch unfortunately. Thanks for all your messages!"
Werner was part of the Germany squad at the 2018 World Cup and EURO 2020.
He has scored 24 goals in 55 caps for the Die Mannschaft.
