A Reuters reporter said armoured vehicles smashed through one of walls of the compound and that he heard bursts of gunfire and grenades.
Colonel Yuliy Mamchur, the commander of the base, said a Ukrainian serviceman had been injured and that he himself he was being taken away by the Russians for talks at an unspecified location.
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Belbek was one of the last military facilities in Crimea still under Ukrainian control following Russia's armed takeover and subsequent annexation of the peninsula, which has a majority ethnic Russian population and is home to one of Russia's biggest naval bases.
Earlier, the deputy commander of the base, Oleg Podovalov, said the Russian forces surrounding the base had given the Ukrainians an hour to surrender.
After the Russians entered, a Ukrainian officer who identified himself only as Vladislav said: "We did not provoke this, this was brute force. I do not know whether this base will be formally in Russian hands by the end of the day.
"Ever since World War Two, this place has been quiet, and they came in here firing, with APCs and grenades. I am very worried now."
Mamchur, the commander, told his troops he would inform the high command that they had stood their ground. The soldiers applauded, chanting "Long live Ukraine!"
Many stood to take pictures of each other in front of the Ukrainian flag, which continued to fly over the base.
The Russian takeover of Crimea has been largely bloodless, though one Ukrainian serviceman was killed and two others wounded in a shooting in Simferopol earlier this week.
Ukraine's Defence Ministry said on Friday that Crimea's bases were still formally under Ukrainian control, but most are now occupied by Russian troops and fly Russia's tricolour flag.
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