The new "agreed upon" chief minister is Abdul Quddus Bizenjo, who won his seat from Awaran with only 544 votes.
Speaker Raheela Hameed Durrani made the official announcement.
The election took place amid beefed up security in and around the assembly building.
A total 54 votes were polled by the lawmakers and Pashtunkhwa Milli Awami Party's (PkMAP) Agha Syed Liaquat Ali bagged 13 votes.
"I will reach out to all political parties, including PkMAP and NP for parliamentary consultation and we will try to resolve issues in the province by keeping everyone together", said the newly-elected chief minister.
He thanked the House for electing him as Leader of the House with an overwhelming majority.
Sanaullah Zehri belonged to the ruling Pakistan Muslim League (Nawaz) but was a tribal leader used to autocratic ways, seldom found in Quetta and spending more time in Karachi like all other Baloch leaders.
Born in 1974, the Pakistan Muslim League-Quaid first became a lawmaker in 2002 and remained Deputy Speaker from 2013-15. He was elected from the PB-41 constituency.More news: National Football League to consider knee injury during concussion protocol investigation
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However; National Party has refused to support the nominated candidates.
On Wednesday, a group of opposition parties in the Balochistan Assembly announced they would not field a candidate for the leader of the House. Balochistan governor will administer oath to the elected Chief Minister.
PML-Q's Bizenjo had earlier in the day been voted in as the third chief minister of Balochistan in four years in a session of the provincial assembly.
In order to retain his position as chief minister, Zehri required the support of 33 members from a house of 65.
On January 2, Bizenjo and 14 like-minded members of Balochistan Assembly submitted a no-confidence motion against Sanaullah Zehri of the PML-N, triggering a political crisis in the province.
Zehri stepped down last week after opposition benches filed a no-confidence motion against him.
Former chief ministers Sanaulla Zehri and Abdul Malik received 9421 votes and 4539 votes respectively during general elections. The crisis was averted on January 9 after Zehri tendered his resignation to Governor Muhammad Khan Achakzai minutes before the no-confidence motion against him.