From March 30, the German carrier will run flights from Frankfurt, with a short stop in Kuala Lumpur (KL) before flight LH 782 continues to the Indonesian capital.
Direct flights to KL will also now take place, as until now travellers could only travel four times a week with a stopover in Bangkok.
Lufthansa will run five weekly non-stop flights Thursdays to Mondays to the Malaysian capital.
This will bring its total number of flights to Asia from Germany to 127 weekly flights and 22 different destinations.
Kay Kratky, member of the Lufthansa German Airlines Board for operations & hub Frankfurt, said: “Indonesia and Malaysia are important countries for business and leisure travel and we are confident that our customers will appreciate the new travel opportunities to south-east Asia and enjoy using them.”