Ukrainian President Viktor Yanukovych issued pardons for former Interior Minister Yuri Lutsenko and former Environment Minister Heorhiy Filipchuk.
Lutsenko was serving a four-year prison term on charges of embezzlement. Filipchuk was sentenced in 2012 to three years in prison for abusing his authority.
Stefan Fule, the European commissioner for neighborhood policy, welcomed the decision.
"This in an important step by the Ukrainian authorities in addressing the concerns regarding the matter of selective justice," he said in a statement.
The European Union said matters of selective justice and democratic progress must be addressed by Ukraine if it wants to move closer to the bloc.
Both leaders served under former Prime Minister Yulia Tymoshenko, who is serving a seven-year prison sentence on similar charges. She remains behind bars.
"We now look forward to Ukraine addressing without further delay the outstanding case of selective justice," Fule said.
Fule didn't mention the Tymoshenko case specifically.