Legislators from the previous parliament had struggled for supremacy against newly elected rivals since Akayev's government was overthrown last week.
Several days of turmoil ensued as the country was caught between different claims of legitimate governance.
The old parliament's upper house ended its defiance and disbanded on Tuesday, one day after a similar move by its lower house, deferring to a new legislature packed with lawmakers who had Akayev's support during the disputed elections that fuelled the push for his ouster.
The move apparently signalled a measure of accommodation between the old elite and the former opposition leaders now in charge of the country, who swung their support behind the new parliament and called for the old one to disband.
The chamber's speaker, Muratbek Mukashev, read a statement signed by 32 lawmakers saying the 45-seat house would end its work to avoid further conflict.
''We believe that we have fulfilled our task, especially during the difficult time for our country,'' Mukashev said.
Interim leader Kurmanbek Bakiyev praised the move. ''You have taken the right and historic decision. I hope your decision will bring calm,'' he said.
A new presidential election
is scheduled for 26 June
Opposition-led protesters had risen up against Akayev's government over allegations of vote-rigging in parliamentary elections held in February and March, and many opposition supporters felt the newly elected legislature should be overthrown along with Akayev.
The old parliament had reconvened hours after the Thursday's takeover, and won the blessing of the Supreme Court.
But the new parliament secured the backing of the country's election commission over the weekend, and at the height of the conflict, the two parliaments held competing sessions on separate floors of the same building.
In recent days, the country's new opposition dominated leadership began leaning towards favouring the new parliament.
Bakiyev - a former opposition leader - had been chosen acting president and prime minister by the old parliament.
On Monday, the new legislature named him prime minister as well, and he declared the new parliament Kyrgyzstan's legitimate legislature.
Bakiyev is a veteran member
of Kyrgyzstan's opposition
A new presidential election is scheduled for 26 June.
About 150 protesters gathered outside the legislature on Tuesday while lawmakers met inside, some demanding the new parliament dissolve and others asking that results for disputed districts be annulled.
But the protesters soon dispersed.
Bakiyev, who maintains that about 20 of the 75 seats in the new parliament are in dispute, reiterated pledges that those races would be reviewed by the courts and Central Election Commission.
''We cannot dissolve the whole parliament,'' he said.
The parliamentary dispute had threatened to plunge the impoverished nation of five million people deeper into crisis after the ouster of Akayev, whose popular support dwindled during a 15-year rule, marked by increasing authoritarianism and corruption allegations.
Akayev fled to Russia last week after the protesters seized his headquarters.
''We believe that
we have fulfilled our task, especially during the difficult time for
old Kyrgyzstan parliament Upper House Speaker
The opposition accused Akayev's government of manipulating the elections to give him a compliant legislature so that he sould stay in power longer than allowed under the constitution.
Kyrgyzstan is the third former Soviet republic in the past 18 months - after Georgia and Ukraine - where the opposition was swept to power after mass protests against long-entrenched leaders.
Strategically located, it hosts both US and Russian military bases and has aimed to cultivate good relations with both countries.