Coach Wallace Tan's boys took a 2-0 lead off Mohamed Zulhamizan (eighth) and Nik Rosemi Aiman (14th) but Austria drew level with goals from Binder Oliver (26th) and Kaltenbock Peter (41st) to take the match into shoot-out.
After a 2013 high of finishing fourth in the New Delhi JWC, the national juniors could not make use of the late entry when Pakistan could not make the trip due to visa problems.
In the Kuantan Junior Asia Cup in 2015, Malaysia had finished fifth among Asian teams after losing out to South Korea in a two-minute blitz, but could not show the same form in Lucknow.
In fact, only hosts India is carrying the Asian flag as they will play against Belgium in the final today.
India were champions in Kuantan, while Pakistan won silver, South Korea bronze and Japan fourth -- to qualify for Lucknow.
However, Japan finished 13th while South Korea 14th and 11th placed Malaysia indicate that the European teams have taken a massive lead in the junior level as well.