Cavendish, victorious in the race in 2007, 2008 and 2011, was not named in Team Dimension Data's squad due to an injury to his right ankle sustained during Tirreno-Adriatico prior to his last race in Milan-San Remo on March 18.
The 31-year-old will also miss the Paris-Roubaix on Sunday.
"Mark sustained an overuse injury of his right ankle while competing at the Tirreno-Adriatico race," said Dimension Data team doctor Dr Jarrad Van Zuydam in a statement.
"The injury was thought to be resolving but has unfortunately flared up again during training. Further investigation and treatment is necessary over the coming days to resolve the injury before Mark returns to racing.
"We are hopeful of a speedy recovery, though it would be premature to set a date for his return to racing at this stage."
In Cavendish's absence, defending champion Kittel claimed his fifth victory from the last six editions of the race.
The Quick-Step Floors rider was towards the leading group of what was a pacey peloton throughout. A crash with four kilometres to go took down a huge number of riders near the front but Kittel avoided the accident.
Team Sky led into the final turn for Elia Viviani but Kittel was tucked into a perfect position ready to strike, and he took the sprint comfortably ahead of Viviani, with Nacer Bouhanni (Cofidis) in third place.
Read the original article on Eurosport: Kittel wins Scheldeprijs as injured Cavendish misses race