Rubio, who had pledged to exit politics when his presidential bid failed earlier this year, defeated businessman Carlos Beruff in the Republican Senate primary. He now faces Democratic Congressman Patrick Murphy in the November general elections.
According to media reports, 45-year-old Rubio is expected to win the November elections, helping the Republican party retain its majority in the US Senate.
If elected, this would be Rubio's second term.
Former Democratic National Committee chairwoman Debbie Wasserman Schultz also won her Congressional primary in Florida.
A Senator is elected directly by the people for a six-year term. Every two years, one-third of US Senators are up for election.