Bernier began playing professional baseball in the Puerto Rican League. He set a league record of 41 stolen bases in the 1949-50 season that was not broken for 32 years until Rickey Henderson bested him with 42 in 1981.

In his first PCL season Bernier platooned at both shortstop and in the outfield in the Pacific Coast League, with Hollywood in 1952, Bernier scored a PCL record 105 runs with 9 home runs. He had career highs as well, racking up 65 stolen bases, and 79 RBIs.

There is some disagreement among historic sources about Bernier's whereabouts in the major leagues in 1953. It was his one major league season. He was drafted in 3rd round, 49th overall pick, by Boston in 1953. He was with the Red Sox for 95 games in 1953 with 3 HR and 31 RBI and a.213 average. He had his first major league hit on April 24th of that year, off pitcher Bill Macdonald of Texas. He was dealt to the Pirates some time that season.

Bernier hit three triples in a row, part of a 12–4 victory over the Redlegs, the team's 4th straight win. Bernier also dinked a single and picked up a stolen base in that game. He hit his first major league homerun on June 22nd off Orioles hurler Bob Malloy.

He returned to Hollywood in 1954 to play outfield for the Stars. He appeared in 119 games with a .313 average in 431 at-bats. While his average dropped to .279 in 1955, he hit a career-high 12 home runs. Beginning in 1955 he was used both as a 3rd baseman and an outfielder. 1957 was his final season with the Stars. During that time he was .292 with 33 home runs and 299 RBIs in 2,734 at-bats in 743 games.

An Angels fan's memory of Bernier:

"MY G-PA USED TO TAKE ME TO ANGEL GAMES ALL THE TIME... AND WE WOULD ESPECIALLY GO WHEN THEY PLAYED THE DREADED "STARS". THE STARS HAD A SHORTSTOP NAMED CARLOS SOMETHING. WE ALWAYS THOUGHT HE WAS A REAL DIRTY PLAYER." - Fan Memoir

In 1958 Bernier played with the Salt Lake Bees (The relocated incarnation of the Hollywood stars, who were moved with the coming of the Brooklyn Dodgers to LA), setting a team-record with a 35 game hitting streak, passing fellow HOF inductee Paul Strand's record of 32 set in 1922.

In 1961 a Sacremento club fleeing the diminishing attendance caused by the Giants move to San Francisco settled down in Hawaii. He won the PCL batting crown in their first season,1961, hitting .361 for Hawaii. In 1962 Bernier hit .313. Carlos played for the team from 1961 through 1964.

He is the first Islanders player to earn induction to the PCL Hall of fame.

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