He made the announcement in an emotional Senate floor address, during which he took direct aim at Trump, striking a tone of defiance and frustration with the state of affairs in Washington.
"I rise today to say, enough," Flake said. "We must dedicate ourselves to making sure that the anomalies never becomes the normal, with respect and humility. I must say that we have fooled ourselves for long enough that a pivot to governing is right around the corner, a return to civility and stability right behind it."
He added, "I will not be complicit or silent. I've decided to better represent the people of Arizona and to better serve my country and conscience by freeing myself of the political consideration that consumed far too much bandwidth and cause me to compromise too many principles."
Flake went on to decry the "regular and casual undermining of our democratic norms and ideals," pleading with his colleagues to cast aside personal provocations and careerism in favor of the best interests of the country.
"We must never meekly accept the daily sundering of our country — the personal attacks, the threats against principles, freedoms and institution, the flagrant disregard for truth and decency, the reckless provocations, most often for the pettiest and most personal reasons, reasons having nothing whatsoever to do with the fortunes of the people that we have been elected to serve," he said. "None of these appalling features of our current politics should ever be regarded as normal. We must never allow ourselves to lapse into thinking that that is just the way things are now."
In his most stinging remarks directed at Trump, Flake criticized the president's leadership — upon which Trump chiefly campaigned last year — and bemoaned his unwillingness to recognize his shortcomings.
"When a leader recognizes new hurt and goes to look for someone to blame, there is perhaps nothing more devastating to a society," Flake said. "Leadership knows that most often a good place to start in assigning blame is to look somewhat closer to home."
In an interview with The Arizona Republic published shortly before his speech, he detailed his beliefs about a forthcoming campaign in which he already has a challenger from his right.
"The path that I would have to travel to get the Republican nomination is a path I'm not willing to take and that I can't in good conscience take," Flake told the newspaper. "It would require me to believe in positions I don't hold on such issues as trade and immigration, and it would require me to condone behavior that I cannot condone."
The Trump-Flake relationship
Flake, Arizona's junior senator, has shown a willingness to criticize Trump since the 2016 presidential campaign.
The senator was one of the first Republicans to publicly voice hesitancy about Trump after he captured the party's presidential nomination. Flake said in July 2016 that he wanted "to support our nominee … but given some of the statements that have been made, I'm finding it difficult."
In August he wrote in a book that the Republican Party has not done enough to keep the executive branch in check. His criticism included calling the administration "erratic," and he bemoaned his fellow Republicans for overlooking their responsibility to maintain a balance in the federal government the way they did when Democrat Barack Obama was in office.
"If I have been critical, it is not because I relish criticizing the behavior of the president of the United States," Flake said Tuesday. "If I have been critical, it is because I believe it is my obligation to do so. And as a matter of duty and conscience, the notion that one should stay silent and as the norms and values that keep America strong are undermined and as alliances and agreements that ensure the stability of the entire world are routinely threatened by the level of thought that goes into 140 characters, the notion that we should say or do nothing in the face of such mercurial behavior is ahistoric and profoundly misguided."
Over the summer, Trump tweeted his approval that Kelli Ward announced a challenge to Flake in the state's Republican primary. Trump said in 2016 that he hoped Flake would lose his re-election bid, although Flake was not on that year's ballot.
At Tuesday's White House press briefing, shortly after Flake's speech, press secretary Sarah Sanders addressed his announcement in positive terms, saying, "Based on the lack of support he has in Arizona, it's probably a good move."
What's next in Arizona
With the incumbent out of the running in 2018, Democrats will likely view his Senate seat as a prime pickup opportunity.
The Democratic Senatorial Campaign Committee has already endorsed Rep. Kyrsten Sinema, who announced her candidacy for the party's nomination in late September. Sinema — who represents Arizona's 9th Congressional District, east of Phoenix — sent a tweet with a link to a fundraising page shortly after Flake's announcement, urging her supporters to "do everything we can to show that we are ready to win."
Ward — who lost a primary challenge against Sen. John McCain in 2016 — is thus far the only candidate for the GOP nomination. She issued a statement after Flake's speech tying her campaign to Trump.
"Arizona voters are the big winner in Jeff Flake's decision to not seek re-election," read the statement. "They deserve a strong conservative in the U.S. Senate who supports President Trump and the 'America First' agenda."
ABC News' John Verhovek contributed to this report.