Reports say at least one person was injured during the assault on Belbek base, near Sevastopol. The base is now said to be under Russian control.
Earlier, several hundred unarmed protesters seized a Ukrainian naval base at Novofedorivka, western Crimea.
Pro-Russian militia have also been seizing Ukrainian navy ships.
Ukrainian troops in Crimea feel beleaguered and abandoned by their commanders in Ukraine.
On Friday, Russian President Vladimir Putin signed a law formalising Russia’s takeover of Crimea from Ukraine, despite fresh sanctions from the EU and the US.
In Belbek, two armoured personnel carriers burst through the wall of the base followed by Russian troops firing weapons in the air.
An ambulance was then seen entering the base amid reports that at least one person had been injured.
The Ukrainian soldiers were later gathered at the base main square in front of the heavily armed Russian troops.
The storming followed an ultimatum by the Russians to surrender.
The Belbek base commander earlier told the few dozen troops still there to shoot in the air if they were attacked.
Ukraine’s military chiefs deny this, saying each unit in Crimea has been issued with clear orders on what to do if attacked.
In Novofedorivka, attackers threw smoke bombs at the base.
Pro-Russian militia – backed by Russian forces – have already seized a number of Ukrainian bases in the southern peninsula.
Russian troops have taken over control of Crimea following last month’s overthrow of Ukrainian President Viktor Yanukovych after mass street protests.
The Kremlin says it acted to protect its “compatriots” in Crimea from “fascists” moving in from the mainland Ukraine.
Kiev denies the claim, accusing Moscow of “blatant lies” to justify the land grab.
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