The European Union, which has curbed its ties with Ukraine over the jailing of Yanukovich opponents, hailed the pardons for former interior minister Yuri Lutsenko and former ecology minister Heorhiy Filipchuk as an important initial step in addressing what it considers "selective justice".
The pardons were the first sign of any relaxation in a drive against Tymoshenko and her allies in which several of her ministers have been jailed or fled abroad to avoid prosecution.
The two former ministers had been serving jail terms for abuse of office. Their pardon came after a week of political tension which saw the opposition, re-energized by a strong showing in an election last October, block parliamentary proceedings and force pro-Yanukovich deputies to hold a rival parliamentary session in a separate building.
The United States and the EU say prosecutions of Tymoshenko and former members of her government are politically motivated.
The EU has made their release a condition for signing deals on trade and political association with Kiev, and has said those agreements could be shelved for years unless progress is made on justice and other issues by next month.
"Ukraine: AT LAST-Welcome very much Pres Yanukovich decision 2 pardon Lutsenko & Filipchuk: first but important step 2 deal w/ selective justice," the EU's enlargement commissioner, Stefan Fuele, wrote in a message on Twitter after the pardon.
According to the presidential decree, Yanukovich's clemency decision was based on a request by the state ombudsman and took into account the health of the two men.
Lutsenko, 48, had been serving a four-year sentence at a jail 230 km (140 miles) north of Kiev and only last week had his appeal against conviction rejected by a court. His press secretary said he had already been released and his wife and a group of supporters were on their way to pick him up.
Despite Sunday's decree, Yanukovich showed no signs of clemency towards Tymoshenko, who is serving a seven-year jail sentence also for abuse-of-office.
The peasant-braided, 52-year-old former heroine of Ukraine's 2004 "Orange Revolution" street protests came close to beating Yanukovich in a bitter run-off for president in February 2010 and is regarded as his fiercest challenger.