Cavendish was participating in the 15km scratch race and had the lead on the final circuit around the velodrome as part of a five-man breakaway which lapped the field. Dutchman Wim Stroetinga finished ahead of the rider from the Isle of Man with Belgian Champion Moreno Peacock third.
On Saturday, Cavendish will combine with Owain Doull in the madison.
Competing at the event qualifies Cavendish for the Track World Cup which he will need to race in order to earn enough points to gain selection for the Olympic Games in Rio de Janiero in 2016. When registering for the International Belgian Open, Cavendish's road team Omega Pharma-Quick-Step reportedly did not know of his intentions.
Cavendish is a two-time world champion on the track, winning the madison in 2005 and 2008.
On Friday, he was named as a starter for the Tour of Britain which begins September 15. While the course does not suit his strengths as a sprinter, Cavendish has indicated he wants to aid Chris Froome's bid for the UCI Road World Championships.
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