The Dimension Data rider, competing for Great Britain, missed out on a medal despite a valiant attempt to haul himself into the top three in the final event of the two-day event – the points race.
Cavendish sat fourth overall after the first day of the competition. He finished second in the scratch and elimination races but finished in 16th in the individual pursuit.
On the final day of the competition he opened up with 11th in the kilometer time trial and fourth in the flying lap. That left him with a chance of taking a bronze if he could overhaul Lasse Norman Hansen, the Olympic omnium champion.
Cavendish started strongly, winning one of the opening sprints. That moved him into provisional third behind leader Kazakh Zakharov and Thomas Boudat of France.
However Hansen, formerly of Cannondale-Garmin, responded with a blistering show of timed aggression and moved back into third. Cavendish was able to hang onto fourth overall and was pleased with his performance.
"I'm really pleased, personally," said Cavendish. "I did better than I thought I was going to do. I'd have been happy with a top ten here so to get fourth..."
"It's been a great group atmosphere - we've won the weekend, won the world cup overall so it's nice to be a part of that."
Cavendish will return to the road later this month with his trade team but with the World Track Championships around the corner he and his coaching staff must plot his next move as he looks for a seat on the plane to the Rio Olympic Games. Last week Shane Sutton told Cyclingnews that Cavendish could ride the Madison at the Worlds in March with Bradley Wiggins instead of competing in the Omnium.