Czech Republic pair Jakub Vadlejch, coached by world record holder Jan Zelezny, and Petr Frydrych threw personal bests of 89.73 and 88.32 metres respectively to take silver and bronze.
Vetter's opening throw of 89.89 was enough to win the gold and the 24-year-old was overcome with emotion after clinching the title which was confirmed after Vadlejch's last throw.
Roehler, who like compatriot Vetter has thrown over 90 metres this season, was beaten into fourth with 88.26.
"I was shaking until my last attempt because I had used all of my energy in the first two throws," said Vetter who was fourth at the Rio de Janeiro Games.
"Technically they were not perfect. I thought I could throw further. It does not matter how far you throw. I threw enough for a gold medal."
"It was very emotional for me at the end of the competition because of the pressure in the last few weeks and days -- it was very high."
Roehler and Vetter have sustained an impressive rivalry this season with Roehler winning six of their 10 meetings before London.
Roehler began the season in Doha with the second longest throw in history of 93.90 until he was overhauled by Vetter's 94.44 metre effort in Lucerne on July 11.
With Andreas Hoffman also in form, Germany even had hopes of a first-ever javelin clean sweep at the World Championships, but the Czech pair had other ideas.
Vadlejch threw 89.73 with his second attempt, while Frydrych left his best for last as he pipped Roehler to the bronze with his sixth throw.
"When my coach Jan Zelezny saw the throws, he was not satisfied and saw many mistakes in it," said Vadlejch. "It was not the worst but you can always go further. The main thing is that I managed to improve my personal best."
"I was dreaming about this medal but now, it is a mixed feeling. Happiness mixed with a bitter feeling that there were these 16 centimetres missing for gold."
(Editing by Ed Osmond and Ken Ferris)
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