His refusal to implement those sanctions had drawn bipartisan ire in Congress, but authorizing them now has enraged Turkey, including Turkish President Recep Tayyip Erdogan, amid deteriorating relations between it and its Western allies like the U.S.
The sanctions, announced by the U.S. Treasury Monday, targeted Turkey's defense procurement agency, known as the Presidency of Defense Industries, and its senior officials, including its president.
Congress was about to force Trump's hand, passing its annual defense policy bill last week that required the White House to implement these sanctions within 30 days -- although a senior State Department official denied that had an impact on Trump's decision.
Turkey acquired the missile defense system, known as the S-400, in July 2019. The purchase violated a sweeping sanctions law passed in summer 2017 by wide margins in the House and Senate to force Trump to be tougher on Russia. Trump, who wanted to avoid an embarrassing veto override, begrudgingly signed the law.
The Countering America's Adversaries Through Sanctions Act, or CAATSA, targeted Iran, North Korea, and Russia -- requiring sanctions on any country that made a "significant purchase" of defense or intelligence equipment from Moscow.
"Today's action sends a clear signal that the United States will fully implement CAATSA Section 231 and will not tolerate significant transactions with Russia's defense and intelligence sectors," Secretary of State Mike Pompeo said in a statement.
"I also urge Turkey to resolve the S-400 problem immediately in coordination with the United States. Turkey is a valued Ally and an important regional security partner for the United States, and we seek to continue our decades-long history of productive defense-sector cooperation by removing the obstacle of Turkey's S-400 possession as soon as possible," he added.
Before today, the Trump administration had only used those sanctions once, penalizing China's defense procurement agency for its own S-400 purchase, along with Russian Sukhoi Su-35 combat aircraft.
After Turkey acquired the same missile system, Trump kicked the country out of the F-35 program, America's most sophisticated stealth fighter, including its role in helping produce the aircraft. At the time, the Pentagon said that Turkey's S400 would jeopardize the F-35's and harm NATO's ability to cooperate militarily -- something Turkey has denied.
Since Turkey's purchase, Republicans have joined Democrats in urging Trump to go further and sanction Ankara, which the president, who has called Erdogan a friend, refused to do. U.S. officials previously said that sanctions could be avoided if Turkey didn't employ the missile system, but Turkish officials test-fired it this October.
Sen. James Risch, R-Idaho, the chair of the Senate Foreign Relations Committee, called Monday's sanctions "long overdue."
In the face of that bipartisan pressure, Trump had repeatedly backed Erdogan in blaming the Obama administration for refusing to sell Turkey the U.S. Patriot missile defense system, which Trump argued forced Erdogan to turn to Russia instead.
"It's a mess. It's a mess, and honestly, it's not really Erdogan's fault," Trump said in 2019 when Russia began delivering the S400. "I think he was unfairly treated."
But that is not true, with Turkey given several opportunities to purchase Patriot missiles over the years, according to lawmakers and current and former U.S. officials.
"Unfortunately, Turkey turned down every single one of these efforts over literally several years now and many engagements and many alternatives offered, leaving us with no choice ultimately," Trump's top diplomat for arms control, Assistant Secretary of State for International Security and Nonproliferation Chris Ford, said Monday.
Asked about reports that Trump long opposed sanctions to avoid upsetting Erdogan, Ford declined to comment, telling reporters during a briefing that he wasn't "in a position to unpack the alleged or actual internals of our deliberative process for you."
Erdogan condemned the U.S. decision Monday, saying, "We expect support from our NATO ally, the United States, in our fight against terrorist organizations and the forces that have account for our region, not sanctions," according to CNN Turk.
The Turkish Foreign Ministry vowed to take "the necessary steps against this decision," adding in its statement that Trump has "admitted on many instances that Turkey's acquisition was justified."
Monday's sanctions include banning all U.S. export licenses to Turkey's Presidency of Defense Industries, also known as SSB, as well as freezing the assets of and banning U.S. visas for its president Ismail Demir and other senior officials.
"Any decision taken abroad towards me or our institution will not change the stance of me and my team; It will not be able to prevent the Turkish defense industry in any way," Demir said of the sanctions in a tweet Monday.
In addition, SSB will be prohibited from receiving U.S. export licenses, loans greater than $10 million from U.S. banks, assistance from the U.S. Export-Import Bank, and loans from international financial institutions like the World Bank.
Although more senior Turkish officials weren't also sanctioned, Ford said that targeting SSB was a "significant step," particularly against a U.S. ally. The delay between Turkey's procurement and U.S. sanctions is "a sign of how carefully we have tried to think this through in ways that hopefully will allow us to preserve a very good and constructive relationship with our ally, while yet sending the signal that there is certain behavior that we cannot accept," he added.
ABC News's Engin Bas contributed to this report from Istanbul.