Daubert was born in Shamokin, Pennsylvania, and began working as a coal miner at age 11. He started his minor league career as a pitcher before settling in at first base; he was signed by the Cleveland Indians in 1908, but didn't hit well enough to make the team, and his contract was sold to Brooklyn. After hitting .264 as a 1910 rookie, finishing among the NL's top five players in triples and home runs, he hit over .300 in each of the next six seasons, usually batting second. On May 6 of his rookie year, he came within one putout of a major league record by recording 21 outs. When the Chalmers Award - the sport's first true MVP award - was created in 1911, he finished in the top ten in the voting in both 1911 and 1912 before winning in 1913. In 1916 he batted .316, finishing second in the batting race behind Hal Chase, as Brooklyn won the NL pennant and went to their first World Series; but he hit only .176 in the five-game loss to the Boston Red Sox. He was nearly the hero of Game 1, however: Brooklyn was trailing 6-1 going into the 9th inning, and after Daubert walked to open the inning, the team scored four times to pull within a run; he came to bat again with the bases loaded and two out, but hit a sharp ground ball which shortstop Everett Scott barely reached. Daubert later had three hits, including a triple, in a 4-3 Game 3 victory.

After slipping to a .261 average in 1917, he bounced back to a .308 mark in 1918, and led the NL in triples (15). When the season was cut short due to World War I and the influenza epidemic, major league owners prorated player salaries; Daubert, who had been among the leading formers of the Players' Fraternity in 1912, sued for the balance, and eventually recovered most of the $2,150. In retaliation, Brooklyn owner Charles Ebbets traded him to Cincinnati for outfielder Tommy Griffith in February 1919, and he became the Reds' captain for the remainder of his career. Although he hit only .276, he was second in the league in runs (79) and third in triples (12), and the team won its first pennant since it debuted in the inaugural season of the American Association in 1882. In the scandal-tainted 1919 World Series against the Chicago White Sox, he batted .241; in the 9-1 Game 1 victory, he had three hits including a triple, and he had two hits and scored twice in the final 10-5 victory in Game 8.

He continued his career by hitting over .300 in the next three seasons, including a .336 average in 1922, when he again led the NL in triples (22) and had a career-high 12 home runs. By 1923, at age 39, he was the oldest regular position player in the major leagues, and he hit .292 that season and .281 in 1924, when he was almost named Cincinnati's manager following Pat Moran's death. After leaving the team due to illness late in his final season, he died in Cincinnati at age 40 from complications following an appendectomy one week earlier. In his career, he had 56 home runs, 1117 runs, 722 runs batted in and 250 doubles, as well as 251 stolen bases. His Brooklyn franchise record of 1206 games at first base was broken by Gil Hodges in 1956.

Daubert was inducted into the Cincinnati Reds Hall of Fame in 1966.