But despite the disruption, the chamber managed to pass the agreement. Russia's state Duma also ratified the deal in a unanimous vote.
The approvals came a week after Dmitry Medvedev, the Russian president, and Viktor Yanukovych, his Ukranian counterpart, signed the deal over the navy base in Ukraine's Crimea region.
But Ukraine's opposition has criticised the renewal of the lease as a historic surrender of sovereignty.
Betrayal of interests
Ukrainian nationalists led by Yulia Tymoshenko, the former prime minister, and Viktor Yushchenko, the former president, regard the base deal as a betrayal of Ukraine's national interests.
They wanted to remove it when the existing lease runs out in 2017.
Several politicians shouted "Shame, shame!" during Tuesday's debate as the parliament ratified the pact, with some 236 of the 450 seat chamber voting in favour.
Deputies also started fighting over a large Ukrainian flag in the middle of the chamber, twisting and distorting the yellow-and-blue banner as smoke continued to billow in the chamber.
Amid the chaos, some deputies tried to carry on with their business, with speakers taking to the floor.
Outside the building, thousands of supporters of Ukraine's former pro-Western government condemned the decision, shouting "Death to Traitors" and "Crimea is Ours".
A counter-rally was also staged, with demonstrators brandishing banners with slogans such as "Ukraine and Russia: Strategic Partners".
Alexander Pikayev, deputy head of the committee of scientists for global security, based in Moscow, told Al Jazeera that the "strategic position" of the naval base was important to Russia.
"Whoever has major a naval base in Crimea actually has control over the whole sea. Secondly, the Russian coast doesn't have a base suitable to deploy a Russian Black Sea fleet and they would have to invest maybe a $1bn to build an autonomous base there.
"During the last several years, we've seen such scenes like today every two months, but what's new is that the Ukrainian parliament adopted the agreement so quickly - within seven minutes, so that's the surprise here," he said.
Russian gas deal
The fleet deal makes Ukraine eligible to receive a 30 per cent discount on gas imports in return for extending the lease on the base in Crimea.
It marks a dramatic turnaround in the country's ties with Russia, which had refused to do business with Ukraine's previous government.
Vladimir Putin, Russia's prime minister, held talks earlier on Tuesday with Ukraine's leadership, offering an unprecedented nuclear co-operation deal and admitting the gas deal had hurt the Russian budget.
"It's going to be a burden, of course. And a major one," Putin said of the gas deal after talks with Yanukovych and Mykola Azarov, Ukraine's prime minister.
"The amount that this has cost us is really something else. For this kind of money I could have eaten Yanukovych and your prime minister together."