34-year-old Cavendish was competing in Poland after being left out of the Tour de France.
Despite crashing on the opening stage he came through the first stages unscathed but has decided to quit the race with two hilly stages to come this weekend.
Cavendish will now turn his attention to Sunday’s Elite Men’s Road Race at the European Championships in Alkmaar.
Cavendish will be up against the likes of Pascal Ackermann, Arnaud Demare, Elia Viviai, Dylan Groenewegen, Alexander Kristoff, Peter Sagan and defending champion Matteo Trentin.
The Time Trial was won on Thursday by rising star Remco Evenepoel.
WATCH - The ride that made Evenepoel European champion
“It was 50 per cent planned, with the Europeans in mind,” Dimension Data’s Alex Sans Vega told Cyclingnews.
“What was 100 per cent certain was that he would do the first three stages and then, depending on how he felt, perhaps go through to the fifth, which is finally what he did.
“He’s been very focused on the race, and, little by little, things are picking up. He’s still needing more race rhythm but I think it’s been very good for his form to be here.
“Obviously it’s up to the British national team coaches to decide on what their strategy will be on Sunday, but I’m sure that if they’re taking him there it’s because they are keen to see what he can do.”