The International Criminal Court said Sergei Shoigu and General Valery Gerasimov deliberately targeted civilians and electricity plants and sub-stations.
The 124 countries signed up to the ICC are duty bound to arrest the pair on sight if they attempt to leave Russia.
Ukrainian human rights ombudsman Dmytro Lubinets said of the warrants: "Sooner or later, a just punishment will overtake every war criminal."
Presidential office chief Andriy Yermak said: "This is an important decision. Everyone will be held accountable for evil."
The warrants came as the Kremlin blamed Washington and warned of retaliation for an attack on Crimea with US-supplied Atacms missiles on Sunday that killed at least four people and injured 153.
However, it is uncertain whether Shoigu and Gerasimov will appear in the dock. The Hague-based ICC does not conduct trials in absentia and it is unlikely they would be handed over by Moscow.
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