Austria captain Janko, who also scored in the 5-0 EURO 2016 Qualifier last week to maintain the nation's four-point lead in Group G, opened the scoring at the Ernst Happel Stadium on 34 minutes.
Marquee man Janko has now scored in nine of his past 10 games for club and country taking his tally to 20 in 45 games for Austria.
Bosnia and Herzegovina replied on 48 minutes through Izet Hajrovic in a game that also saw Bayern Munich - that led to him being replaced at half-time.
In a real flashpoint, Bosnia and Herzegovina captain Edin Dzeko appeared to grab Aleksandar Dragovic by the throat in the after math to a poor challenge from Muhamed Besic - although he was only booked for his actions.