Manu, who had also secured the quota for the 2022 Tokyo Olympics, shot 24 in the final, bowing out in a shoot-off to miss out on another international medal
Already assured of a silver, the Indian duo was on par with Russia's Vitalina Batsarashkina and Artem Chernousov at 12-12 before losing the last two series to go down 12-16.
Earlier, in the 10m air rifle events, the men's trio of Aishwary Pratap Singh Tomar, Deepak Kumar and Divyansh Singh Panwar lost the bronze medal match.
In the individual events, Bhaker will be fielded in the women's 25m pistol, 10m air pistol event with Yashaswini Singh Deswal and in the 10m air pistol mixed event