Lawmakers voted overwhelmingly to dismiss the government of Prime Minister Sapar Isakov, a 40-year-old technocrat viewed as a loyalist of the country's former leader Almazbek Atambayev.
Jeenbekov subsequently signed an order confirming the government's dismissal.
A total of 101 legislators voted for the move with just five against, according to an official parliamentary protocol.
The vote indicated broad parliamentary support for Jeenbekov, 59, who is now expected to play a key role in determining the next premier.
Jeenbekov came to power in a bitterly fought presidential election last year while enjoying strong support from Atambayev, 61, who was limited to a single term in office by the constitution.
But tensions have since emerged between the pair after Atambayev criticised appointments made by Jeenbekov and called for the new president's brother, Asylbek, to relinquish his seat in parliament in a public appearance last month.
Earlier this month Jeenbekov fired key Atambayev allies in the national security service and initiated the sacking of the country's state prosecutor, but has yet to make his own appointments.
Known since his time as an opposition leader for a fiery and often vulgar public speaking style, Atambayev moved the impoverished ex-Soviet country away from the West and closer to traditional ally Russia while in office.
On March 31 he was elected chairman of the Social Democratic Party of Kyrgyzstan that has dominated Kyrgyz politics since a violent revolution ousted authoritarian leader Kurmanbek Bakiyev in 2010, despite initially pledging to leave politics.
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