The scuffles broke out after eggs were thrown at the speaker of the Verkhovna Rada, Volodymr Lytvyn, who then took cover behind two black umbrellas held by aides.
The first smoke bomb was then thrown from an unknown source and the chamber filled with smoke, making it difficult to watch proceedings. Some deputies covered their noses or put on masks as alarms sounded.
A second smoke bomb was thrown shortly afterwards, creating thicker smoke in the chamber as deputies nonetheless continued their rancorous debate, an AFP correspondent in the chamber reported.
The deputies in the notoriously fractious Parliament were taking part in a session debating a controversial deal last week to extend the lease on Russia's Black Sea Fleet naval base in Crimea until at least 2042.
The deal signed last week by Russian President Dmitry Medvedev and his Ukrainian counterpart Viktor Yanukovych had been slammed by the pro-Western Ukrainian opposition as a historic surrender of sovereignty.
Deputies also started fighting over a massive 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 push on with their business as if nothing extraordinary was taking place, with speakers taking to the floor.
With some lawmakers shouting "Shame, Shame!", the Parliament ratified the pact with 236 lawmakers voting in favour of ratifying the deal in the 450 seat chamber.
'Death to traitors'
Meanwhile, thousands of supporters of Ukraine's previous pro-Western government protested outside parliament over the decision, shouting "Death to Traitors" and "Crimea is Ours".
Amid a heavy security presence, supporters of Mr Yanukovych held a counter rally brandishing banners with slogans like "Ukraine and Russia: Strategic Partners".
The fleet deal marked a dramatic turnaround in Russian-Ukrainian ties after the relationship became so bad under Mr Yanukovych's predecessor, the fiercely pro-Western Viktor Yushchenko, that Moscow refused to do business with him.
Under the deal, Russia agreed to give Ukraine a 30 per cent discount on Russian natural gas imports estimated to be worth 40 billion dollars over 10 years. In exchange, Kiev has extended the lease of Russia's Black Sea Fleet base in Crimea for another 25 years after 2017, with the option of another five year extension after 2042.
Russian Prime Minister Vladimir Putin had earlier held talks with Ukraine's leadership, offering an unprecedented nuclear cooperation deal and admitting the gas deal had hurt the Russian budget.
"It's going to be a burden, of course. And a major one," Mr Putin said after the talks with Mr Yanukovych and Prime Minister Mykola Azarov of the gas deal
"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," said Mr Putin.
Underling the strength of Moscow-Kiev ties, he also offered Mr Yanukovych an effective merger of the two countries' nuclear power businesses.