Dignitaries, spectators and more than 36,000 runners observed a moment of silence before the race began.
The heavy security operation included a ban on rucksacks and screening at checkpoints.
US runner Meb Keflezighi and Rita Jeptoo from Kenya won the men’s and women’s races.
Athletes with disabilities were the first competitors to set off, at 08:50 local time.
The elite women’s race started at 09:32, with the elite men setting off half an hour later, followed by thousands of other runners.
Meb Keflezighi won the men’s race, clocking in at 2 hours, 8 minutes and 37 seconds.
He is the first US runner to take the title since 1985.
Rita Jeptoo was the first to cross the finish line in the women’s race, marking her third win in the competition.
She finished the course in a record 2 hours, 18 minutes and 57 seconds.
The 26.2-mile (42.2 km) route was tightly guarded in a massive mobilization of law enforcement agencies, including police units, bomb squads and tactical assault teams from other states.
The Boston police department erected 8,000 steel barricades, 1,200 more than last year.
Many people in the city have been wearing “Boston Strong” T-shirts.
Last year’s winner of the men’s elite race, Ethiopian Lelisa Desisa, was competing again and met several victims of the blast.
Bombing suspect Dzhokhar Tsarnaev, 20, is due to stand trial in November. He has pleaded not guilty to 30 charges, including 17 that carry the death penalty.
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