Freund led at the halfway stage in the Czech Republic and didn't jump again as after various delays, a cancelled trial round and a postponement of the start the winds were deemed too strong.
Sven Hannawald was the last German to win the ski flying world title when he defended his crown in 2002 and Freund admitted to a special feeling despite the nature of his victory.
"I prepared myself to jump because I heard that the weather forecast was better in the evening. Unfortunately we couldn't jump," he said.
"It's always nice to have competitions, but safety is most important. It's my best season and this gold medal is very special."
After only two instead of four rounds silver went to Anders Bardal and bronze to Peter Prevc with Noriaki Kasai fourth and double Olympic and World Cup champion Kamil Stoch fifth.
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- Sven Hannawald