The vote was later annulled but this did not quell the tensions.
"Yesterday, the Kyrgyz Parliament approved the composition of the government, I signed the presidential decrees on the appropriate appointments".
Kyrgyzstan, a country of 6.5 million people located on the border with China, was plunged into chaos following an October 4 vote that election officials say was swept by pro-government parties. Jeenbekov announced last week that he would resign, but this week he delayed his exit, saying he would stay in office until a new election was held.
Populist figurehead Mr Japarov was among prominent figures sprung from jail during the unrest.
Mr Azimov also pointed out that Russian Federation and the West had thrown their weight behind Mr Jeenbekov since the unrest began. Two of his closest allies remain at large.
Following Jeenbekov's resignation, supporters of Zhaparov gathered on the streets to demand the dissolution of parliament and the ouster of its speaker.
One a day earlier, Jeenbekov had refused calls to resign.
"Military personnel and law enforcement are obliged to use weapons to protect the state residence".
"In this case, blood will be shed, it is inevitable", Jeenbekov's statement said. "I urge both sides not to fall for provocations", Jeenbekov said as he chose to step down.
The president had on Wednesday finally affirmed Japarov as prime minister, in a move seen as the first step towards calming the crisis.
The country of 6.5 million people on the border with China was plunged into chaos following an October 4 parliamentary election whose results were a victory for pro-government parties.
On Friday, political leaders, including his main rival, former president Almazbek Atambayev, rallied in Ala-Too Square in the capital Bishkek, but thugs armed with sticks and allied to Japarov attacked and dispersed the crowd.
Jeenbekov also called on Prime Minister Sadyr Zhaparov to withdraw his supporters from the streets and return the country to peace.
"I am not clinging to power", Jeenbekov said in an address to the nation as, by the president's own admission, Kyrgyzstan teetered on the brink of violence. "He's very weak. No spirit", Dastan Bekeshev, a lawmaker who supports neither Jeenbekov nor Japarov, told Reuters. According to the Kyrgyz constitution, Zhaparov would then become the most powerful man in the country.
The prime minister's spokesman declined to comment on whether Japarov would now press the speaker to stand down.
He was serving time for hostage-taking and has been suspected of ties to organised crime, prompting a rally last week.
"Even though there has never been direct evidence of Sadyr Japarov being linked to organized crime", his three and a half years in prison and ill treatment there have many people asking "whether he is still an independent political figure who is not being subjected to any kind of pressure or manipulation from the criminal world", Azimov said.
Jeenbekov is the third president to be overthrown in a popular uprising since Kyrgyzstan gained independence in 1991.
Kyrgyzstan - an ally of Russian Federation that also border China - is one of three former Soviet countries in the middle of massive upheaval, alongside Belarus and the military conflict between Azerbaijan and Armenia.