Malik and Bagri were arrested in 2000 and charged with a list of offences including murder.
British Colombia Supreme Court Judge Ian Bruce Josephson has taken three months to take a decision.
Prosecutors took 13 months to present evidence.
The investigation into the bombing took 15 years.
The prosecution said the men helped plant the bomb on the Air-India plane in revenge for the Indian Army's storming of the Golden Temple.
A second bomb, in luggage to be loaded on to another Air-India flight, exploded the same day at Tokyo's Narita airport.
Two baggage handlers died in the blast.
Relatives crowd airport counters for information on the fateful day.
Photograph: PANA-INDIA