However, it is not clear if his resignation will stop the unrest that has brought chaos to the country since last week. On October 16 the parliament will meet to accept the president's resignation and the picture will become more clear as to who, exactly, will become the acting president.
At the Issyk-Kul hotel, on the southern edge of Bishkek, where Japarov supporters were rallying throughout the day, cries for Isayev's ouster had begun even before Jeenbekov made his announcement.
In further developments, protesters also released former prime minister Sapar Isakov, who had been doing a prison sentence for corruption at the Historical Museum and during the modernization of Bishkek CHPP.
Zhaparov formed a new Cabinet, promised his supporters to push for Jeenbekov's resignation and held talks with the president hours after Jeenbekov signed off on his appointment. After police tried to break up the protests with water cannons, stun grenades and tear gas, the demonstrators regrouped and by dawn on October 6 had stormed several government buildings. "I do not want to go down in the history of Kyrgyzstan as a president who shed blood and shot at his own citizens", Jeenbekov wrote.
Jeenbekov said the situation in Bishkek "remains tense" and that he didn't want to escalate those tensions.
Mr Jeenbekov called on Mr Japarov and other politicians "to withdraw their supporters from the capital of the country so the people of Bishkek can return to a peaceful life".
Parliament must officially approve his resignation.
Jeenbekov had previously pledged to resign after overseeing fresh parliamentary elections in the country. Election officials claim that pro-government parties won the vote. The opposition said the election was tainted by vote-buying and other irregularities.
The result was annulled after protesters seized government buildings on October 6.
Populist politician Japarov was confirmed as head of government on Wednesday, as the Central Asian state sought a path out of 10 days of crisis following an annulled election.
Jeenbekov announced last week that he planned to resign but didn't say when.
Authorities deployed troops to the capital over the weekend and introduced a curfew. The move eased tensions in the city as citizens stopped fearing the violence and destruction that they had experienced with earlier uprisings.
On Wednesday, Jeenbekov accepted parliament's choice of Sadyr Japarov, a nationalist whose supporters freed him from prison last week, to be prime minister.
Japarov had been serving jail time for hostage-taking, but was named prime minister soon after his release.
Jeenbekov accepted Japarov as the new prime minister earlier this week.
Mr Zhaparov was quoted by Kyrgyz media as saying at a news conference that he will continue pushing for Mr Jeenbekov's resignation, which was "the people's demand". The Kyrgyz leader had said he would stay in the job until the political situation had calmed.
He also reaffirmed his commitment to maintain a strategic partnership with Russia and said he had no plans to change the terms of Russian military presence in the mountainous country of 6.5 million which borders China. It is a member of Russian-controlled economic and security agreements.