"We live in a republic and our voters make these decisions," Rubio said in Miami Tuesday night as his supporters booed Trump's victory.
His speech was a thinly veiled rebuke of Trump's campaign tactics, as he warned that it would have been easier for him to exploit the anger and anxiety driving the race. He warned that the politics of division were going to leave America a "fractured nation."
"America is in the middle of a real political storm, a real tsunami and we should have seen this coming," Rubio said.
"While we are on the right side," he said," this year, we will not be on the winning side."
Rubio, the 44-year-old first-term senator, had positioned himself as the only person who could stop Trump, and had gone on the attack, memorably bringing up the size of the Trump's hands during a campaign rally and at a presidential debate.
His campaign slogan was "a new American century" -- as he tried to send the message that America needed a new generation of leadership that could deal with the challenges ahead. It was also a way to spin his relative youth, and short time in the U.S. Senate as an advantage.
He drew heavily from his life story on the trail. The child of Cuban immigrants, Rubio's parents worked menial jobs like bartending and hotel cleaning to provide for their children. His stump speech drove home the message that Americans should leave their children better off than they were, and warned that dream was slipping away.
After not winning any of the early contests, Rubio's advisers and donors banked on him consolidating the establishment vote -- particularly after Jeb Bush quit the race -- and winning in big states like his home of Florida.
Meanwhile, Trump continued to lead the pack and Texas Sen. Ted Cruz became the second favorite, picking up the first contest of Iowa and far more states than Rubio along the way.
Rubio tried several tactics to deal with Trump. At first, he mostly ignored the front-runner, aiming his fire instead for his closest competitors for the nomination like Cruz and Bush.
But as Trump continued to roll, Rubio made a sudden strategy change at the GOP debate in late February in Houston. That night and in successive days, Rubio unleashed a torrent of opposition research combined with schoolyard insults, suddenly mentioning Trump by name and hand size in his stump speeches.
Trump responded in kind, making a crude joke about his penis size at a following debate, and seemed to get the better of the tiff against "Little Rubio," who lost momentum rather than gain it after the attacks.
Rubio's other major stumble came much earlier in the campaign, in the first primary on the calendar. At the New Hampshire debate before the Granite State's contest, Rubio fell into his habit of repeating his one-liners, and New Jersey Gov. Chris Christie mocked him brutally for doing so. The widely panned debate performance was followed by a dismal fifth place finish in that early primary, only made worse by establishment rival Ohio Gov. John Kasich's surprise second place placement.
The Cuban-American did get his mojo back, though, nabbing the highly sought-after endorsement of South Carolina Gov. Nikki Haley to best Cruz for second in that state and Nevada.
And after Bush's departure from the race, a slew of establishment Republicans ran to endorse Rubio, including Haley being joined by the sitting governors of Kansas, Arkansas, Tennessee and New Mexico.
Rubio lost every one of those states, except New Mexico, which has yet to vote.
The campaign has blamed other candidates for some of their troubles, including singling out Kasich as a spoiler. Kasich's share of the vote especially stung in Virginia on Super Tuesday, where Rubio came within 3 percentage points of beating Trump.
But despite his campaign's argument that an establishment candidate could win if the slate of candidates would just narrow, anti-establishment candidates Trump and Cruz only picked up steam in the wake of Rubio's endorsement avalanche, as Rubio fell back to third and fourth place in races.
His last stand came down to his home state of Florida, which was called for Trump as soon as polls closed at 8 p.m.