Embattled Bolivian President Evo Morales fled the capital La Paz and resigned after the head of the armed forces, Gen. Williams Kaliman, suggested that he leave power in the wake of an Oct. 20 presidential vote that electoral monitors said was marred by fraud.

Sunday’s resignation by the 60-year-old leader, who as a union leader helped lead protests that toppled other presidents, came as the armed forces had declared itself neutral after three weeks of increasingly chaotic demonstrations across several cities. In a televised...