American Keeron Clement successfully defended his 400m hurdles crown with a season's best time of 47.91 seconds ahead of Javier Culson.
Greene ran a time of 48.68 seconds but admitted afterwards: "I seemed to run out of steam after 200 metres.
"Usually when I hit 200m I can kick on but I didn't have it in my legs today."
Greene was first at the Spar European Team Championships earlier this year but the 12th World Championships in Germany was the 23-year-olds first major tournament.
But Greene's season's best time of 48.27 seconds ensured the Welshman is the fastest man in Europe in 2009 as expectations grew ahead of the Berlin showpiece.
The Swansea Harrier runner admitted himself: "I came here with the intention of making the final and my expectations were raised when I made it through the semi-finals. But sadly it wasn't to be.