Tovar was born in Caracas, Venezuela. He was signed by the Cincinnati Redlegs in 1959 and, after being traded to Minnesota in late 1964, made his debut on April 12, 1965. The Twins made ample use of his ability to play a variety of positions; by 1967, Tovar divided his fielding season between third base (70 games), center field (64), second base (36), left field (10), shortstop (9) and right field (5), setting an American League record of 164 games played and leading the league with 649 at-bats. In addition, he was among the top 10 batters in runs, hits, doubles, triples, stolen bases, on base percentage, hit by pitch and sacrifice hits. He improved his batting average through 1971, when he batted .311 and led the league with 204 hits. On September 19, 1972 Tovar hit for the cycle, but it was only one of many striking accomplishments in his career.

On September 22, 1968, Tovar became the second player to play every position in a game, joining Bert Campaneris (Kansas City Athletics, 1965), Scott Sheldon (Texas Rangers, 2000) and Shane Halter (Detroit Tigers, 2000). No National League player has ever done it. Tovar started the game on the mound against Oakland and pitched one scoreless inning in which he struck out Reggie Jackson; the first batter he faced was Campaneris.

Tovar is regarded as the all-time AL leader in breaking up no-hit attempts with five. On April 17, 1967, Tovar's single was the only hit against the Washington Senators' Barry Moore. On August 10, 1969, Mike Cuellar of the Baltimore Orioles extended his streak of consecutive batters retired to 35 before surrendering a ninth-inning single to Tovar, which also broke up Cuellar's bid for a no-hitter. Earlier in the season (May 15), he broke up the no-hit bid of another Baltimore pitcher, Dave McNally. Tovar was responsible for spoiling two other no-hitters during his career: against the Washington's Dick Bosman (August 14, 1970) and the Yankees' Jim "Catfish" Hunter (May 31, 1975).

Along with Bert Campaneris, Tovar is one of only two players to have played in all of the baseball positions, including one pitching appearance and being a designated hitter.

In 1967, the Triple Crown Boston Red Sox outfielder Carl Yastrzemski received all but one vote for the American League MVP award; the lone dissenting ballot was marked in favor of Tovar.

On May 18, 1969, Tovar combined with Rod Carew to set a major league record for most steals by a club in one inning with five, in the second inning against a Detroit battery of Mickey Lolich and Bill Freehan. Carew stole 2nd, 3rd and home; Tovar stole 3rd and home ahead of Carew. The two steals of home in the same inning also tied a record.

In 1971, Sport magazine polled major league players to identify the game's most competitive player. Pete Rose won; the runners-up were Frank Robinson, Bob Gibson, and César Tovar.

After a colorful tenure as a Twin, Tovar platooned with the young Mike Schmidt at third base for the Phillies in 1973. After that, he gave the Rangers, Athletics and Yankees, three years of his versatile good services.

In his 12-year career, Tovar batted .278 with 46 home runs, 435 RBI, 1546 hits, 834 runs, 253 doubles, 55 triples, and 226 stolen bases in 1448 games.

César Tovar died of pancreatic cancer in Caracas, Venezuela at 54 years of age.