Lewis was signed by the Tigers in 1959, but was traded to the Cardinals in the same year. He played in the Cardinals' farm system until making his major-league debut with St. Louis in April 1964. He split the '64 season between the Cardinals and their AAA team in Jacksonville. After the season, he was traded to the Mets for pitcher Tracy Stallard.
Johnny was the Mets' everyday right fielder in 1965, playing 100 games there and another 40 games in center field. He also socked 15 home runs, but only bat .245.
In 1966 the Mets acquired veteran outfielder Al Luplow from the Indians, who, along with Larry Elliot took most of the playing time in right field. With Ron Swoboda a fixture in left field, and rookie Cleon Jones in center, Lewis was relegated to the bench as a 5th outfielder and pinch-hitter. He also played 71 games down in Jacksonville.
The Mets obtained left fielder Tommy Davis from the Dodgers before the 1967 season, so Lewis was toast. Johnny played most of the season in Jacksonville, and only 13 games with New York, the last coming on June 11th. He wrapped up his professional career with the Phillies' AAA team in San Diego.