In the 10m air rifle event, Austria's Martin Strempfl finished at the top with 632.5, Sajjanar was second with 630.5 while Etienne Germond of France was placed third with 629.4.
World number one Indian Divyansh Singh Panwar had to be contend with a fourth-place finish with 627.8.
In the 10m air pistol competition, Amanpreet shot 576 to finish at the top with Ashish Dabbas at second place with 575.
Teen sensation Bhaker, who has already secured a quota place for the Tokyo Olympics alongside Divyansh, was third with a score of 572.
Hungary's Veronika Major finished fourth with 569.
A total of 50 shooters from seven countries took part in the innovative event, an initiative of former India shooter Shimon Sharif to help the athletes "get a feel of competition" during the coronavirus-forced lockdown in many countries.
Doing commentary was renowned Hungarian shooter Peter Sidi as marksmen and markswomen turned their homes into shooting ranges.
The competitors logged in through Zoom app from their respective locations and shot using their Electronic Shooting Targets (EST).
The competition was live streamed on the internet.
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