The Syrian government condemned Trump's pledge, saying it flies in the face of international law.
Turkish President Recep Tayyip Erdogan warned of a "new crisis" if the US president tried to officially enact the move.
"After 52 years it is time for the United States to fully recognise Israel's Sovereignty over the Golan Heights," Trump said in a tweet.
Trump called the Golan -- a strategic area seized from Syria and annexed in a move never recognized by the international community -- "of critical strategic and security importance to the State of Israel and Regional Stability!"
Trump says time to recognise Israel's sovereignty over Golan Heights
After 52 years it is time for the United States to fully recognize Israel’s Sovereignty over the Golan Heights, which is of critical strategic and security importance to the State of Israel and Regional Stability!Donald J. Trump (@realDonaldTrump) March 21, 2019
About 20,000 Israeli settlers live in the Golan, which overlooks Syrian territory.
Trump's abrupt announcement was immediately cheered by Netanyahu, who faces a tough re-election battle and visits Washington next week.
"At a time when Iran seeks to use Syria as a platform to destroy Israel, President Trump boldly recognises Israeli sovereignty over the Golan Heights," the right-wing prime minister wrote on Twitter. "Thank you President Trump!"
Trump says US recognises Israeli sovereignty over Golan Heights
There was also quick approval from the senior Republican in the US Senate, Lindsey Graham, who is pushing for Congress to recognize Israeli control over the Golan.
"President Trump's decision to recognize the Golan as part of Israel is strategically wise and overall awesome. Well done, Mr. President!" Graham tweeted.
Trump's announcement coincided with a visit by Secretary of State Mike Pompeo to Jerusalem, where he became the first high-ranking American official to visit the Western Wall alongside an Israeli prime minister -- another boost for Netanyahu.
However, Leon Panetta a veteran Democrat who served as CIA director and defence secretary, among other roles, blasted Trump for "tweeting out another policy that obviously has not been worked out with our international partners."
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The Golan recognition is only the latest diplomatic bombshell dropped by Washington, which is Israel's principal backer, in seeking to redraw the fraught Middle East map.
In 2017, Trump also went against decades of practice in recognizing the disputed city of Jerusalem as Israel's capital, rather than the previously accepted Tel Aviv.
The Golan Heights move was hinted at a week ago when the State Department changed its usual description of the area as "occupied" to "Israeli-controlled."
The Trump State Department has likewise dropped previous definitions of the Palestinian territories of the West Bank and Gaza Strip as being "occupied" by the Jewish state.
Israel occupied the Golan Heights, West Bank, East Jerusalem and the Gaza Strip in the 1967 Six-Day War. It later annexed the Golan Heights and East Jerusalem in moves never recognized by the international community.
During Pompeo's Jerusalem trip, there was also speculation that his Western Wall visit with Netanyahu could be interpreted as tacit approval of Israel's claim to sovereignty over the site. The wall is one of Judaism's holiest spots, but located in mainly Palestinian east Jerusalem.