"It is with a heavy heart that I have to announce that I will be leaving the Giro d'Italia due to COVID-19 after taking a routine test, which unfortunately was positive," Evenepoel, who had regained the Maglia Rosa by winning Sunday's individual time trial, said in a statement.
The new race leader is Britain's Geraint Thomas.
Three-time Vuelta champion Primoz Roglic is second overall, two seconds behind with Thomas's Ineos-Grenadiers teammate Tao Geoghegan Hart in third place, five seconds off the pace.
Ineos Grenadiers were without two-time time trial world champion Filippo Ganna after the Italian tested positive for COVID-19 ahead of stage eight.
Monday is a rest day on the Giro. Tuesday's stage 10 is a 196-km ride from Scandiano to Viareggio, which features a long climb before a fast‑running and technical descent.