Anyone who could not finish the race within 2.5 hours was urged to drop out.
The forecast caused concern on Saturday, with the threat of thunderstorms prompting police to announce possible changes to the lineup of events.
Boilermaker President Tim Reed said in a press conference on Saturday that "rain is not the issue, but thunderstorms are."
Around 5:00 a.m. on Sunday morning runners were told all events would be held, but the post race party would end at 11:00 a.m.
The annual event was expected to draw more than 50,000 racers and spectators.
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