Cheered on by supporters, the runners jogged from Kenmore Square to the finish line, The Boston Globe reported.
"It's a great way to show the strength of Boston and the camaraderie in our city," runner Liza Marie Felici, 28, of Dover said. "There's a sense of closure ... . Yes, it's a month later, but it's happening."
Organizers of the event, called OneRun, said about 3,000 people participated with a large number of police officers guarding the route, the newspaper said.
No incidents were reported.
No security incidents or medical emergencies were reported, according to officials at the finish line.
Also running were MIT campus police officers, whose colleague, officer Sean Collier, was allegedly shot and killed by two bombing suspects in Cambridge, the Globe said. Three people were killed and scores injured when two bombs were detonated near the finish line of the April 15 race.
"It's our chance to just run and show support to the victims," patrolman Karl Martinsen said. "It's a special event. It will be a short run, but emotional.
"It's been hard. Fortunately, the department and all the guys we work with, we're like a family. We've been there for each other, and today is an extension of that."