DPT candidate Dechen Zangmo won the polls in Nanong-Shumar constituency, media reports said.
Zangmo defeated Pema Wangchuk of the ruling People's Democratic Party (PDP).
Thinley, 60, resigned in July, becoming the first person in Bhutan to quit the legislative body.
His DPT party was routed by the PDP in Bhutan's second national election held in July. The PDP won 32 seats in the 47-member National Assembly.
Thinley was one of the 15 DPT candidates who were elected in the recent polls.
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There are 25 seats in the National Council or the upper house. Five of them are appointed by the King and 20 are elected from 20 districts.
Compared to the general election, the number of voters was reduced by 1000 in Nanong-Shumar bye-election. The total number of registered voters for the constituency is 8,247.
Thinley had secured a landslide victory with 3,742 votes against PDP's Wangchuk who got 1011 votes in the polls earlier this year.