But the two fell out and Yushchenko fired Tymoshenko's government in 2005.
The two appear to be allies again, however, with Tymoshenko saying she would meet Yushchenko on Monday to quickly formalise their new alliance.
Together, the former Orange Revolution partners could win enough seats to unseat Yanukovych.
"In one or two days we will announce the coalition," Tymoshenko, smiling triumphantly, told reporters.
Yuriy Lutsenko, the leader of Yushchenko's party, said it was ready to back Tymoshenko as prime minister after the coalition is formed.
A somber-looking Yanukovych made a brief statement in which he tried to present the results as his party's victory, saying it would now start talks with potential coalition partners.
"We consider the election results as a carte blanche for our party to form a new government," he said.
Official results are set to be published on Monday.
Al Jazeera's Jonah Hull reported from Kiev that the Litvin bloc had emerged as the potential kingmaker.
They could go either way. If they support the Orange Revolution coalition, then they get enough of a majority to set up a government.
But if they go with Yanukovych, then there will just be one or two seats separating the two sides, not enough of a majority for either side to set up an effective government.
Blank ballot papers which should have been destroyed, were apparently put into ballot boxes during voting, monitors told Al Jazeera on Sunday.
Ukraine has 37.5 million registered voters but irregularities in voter registration have increased fears there could be legal challenges to any result.
Stephen Woloshyn, a monitor, said he saw more than 10,000 blank ballots at an election office in the eastern town of Donetsk.
"They are trying to add 10,000 votes to the list - which is illegal," said Woloshyn, an election monitor from the Canadian-Ukrainian Association.
Vote-rigging led to the 2004 presidential election result being annulled and the pro-Western Yushchenko sweeping to power after the Orange Revolution.
Polls had opened at 7am (04:00 GMT) and closed at 10pm.
Laurence Lee, Al Jazeera's correspondent in Donetsk, said allegations of vote rigging were coming in from other parts of the country.
"There is potential for this to go to the courts and that could take week and weeks to resolve."
Ukrainians have faced three years of political paralysis as Yushchenko has sought to push Yanukovych from power.
Yushchenko defeated Yanukovych in a re-run of the presidential election in 2004 after the original result was declared invalid in the wake of a series of mass pro-democracy protests that became known as the Orange Revolution.
Since then, however, Yushenko has failed to implement many of the reforms he promised and Yanukovych, who favours closer ties with Russia, has undergone a political resurrection.
After being accused of rigging the presidential vote in 2004, Yanukovych became prime minister after his party won a majority in elections in 2006.
Yanukovych, whose Regions party draws his support from Ukraine's Russian-speaking east and south, fiercely resisted Yushchenko's decision to dissolve parliament in April and call new elections after the president accused him of seeking to seize power.
Yanukovych eventually agreed to the vote on Sunday, but has suggested victory would be the only outcome he is prepared to accept.
Source: Al Jazeera and agencies