The ministry said on its Facebook page that the jets were among four Russian-built fighters that were returning to base after providing air support for Ukrainian troops near the border.
The pilots of both jets ejected from the aircraft, the ministry said. Their condition was not immediately reported.
Defense Ministry spokesman Oleksiy Dmitrashkovsky said the Sukhoi-25 fighters were downed in an area called Savur Mogila in the Shaktersky region near the Russian border.
The site is only a few miles from where a Malaysia Airlines jetliner crashed last week after apparently being shot down by a surface-to-air missile with 298 people aboard.
The latest shootdowns are the first reported downing of a plane over eastern Ukraine since the Malaysia Airlines incident.
A similar SU-25 jet was shot down on July 17, the night before the MH 17 crash, by an air-to-air missile along the country's border with Russia, according to the Andriy Lysenko, a spokesman for Ukraine's national defence and security council.