Connally was commissioned in the United States Naval Reserve in 1941, where he went through nine major air-sea battles in the Pacific. In April 1945 he endured fifty-two consecutive hours of Japanese kamikaze attacks. He was credited as a hero and rose to the rank of lieutenant commander. He returned home to work in politics and worked for Lyndon B. Johnson's 1946 reelection campaign to Congress and his 1948 Senatorial Campaign. There where allegations that Connally had been involved in voter fraud after a suspicious late report of 200 votes in Box 13 from Jim Wells County came in for Johnson, resulting in his 87 vote victory.
In 1961 Connally served as secretary of the navy under President John F. Kennedy. He was elected Governor of Texas the next year. In 1963 he suffered serious gunshot wounds while riding in President Kennedy's car during his assassination, however recovered quickly. Connally was easily reelected Governor in 1964 and 1966.
Although a Democrat, he called himself "a conservative who believed in active government." And in 1971 he became Richard Nixon's Secretary of the Treasury. In 1972 he organized the political action committee "Democrats for Nixon" to support President Nixon's reelection campaign. Connally switched political parties from the Democrat to Republican in 1973. He briefly tested the presidential waters in 1980, but failed to win the Republican Party nomination in part because of a "wheeler-dealer" image from the media. After the election he left politics and returned to private life.