RIO DE JANEIRO — What the vault is to the United States gymnast Simone Biles, the 100-meter butterfly is to the five-time Olympian Michael Phelps. The shortest individual race in Phelps’s Olympic program has always been his toughest. His three consecutive victories, starting at the 2004 Games in Athens, came by a total margin of 28-hundredths of a second.

In his previous three finals, Phelps had never been better than fifth after the first 50. In Friday night’s final, he turned sixth, more than a half-second behind the leader, Joseph Schooling of Singapore, a rising junior and all-American swimmer at Texas.

Phelps chased Schooling in the last 50, but Schooling could not be caught. He clocked a 50.39, faster than Phelps swam in any of his Olympic victories.