Vice President Joe Biden led an emotionally charged tribute at the Hynes Convention Center, just steps from the scene of the attack that left three dead and more than 260 others wounded.
"You have become the face of America's resolve, not unlike what happened on 9/11," Biden told the survivors, relatives of victims and emergency workers who responded to the carnage on April 15, 2013.
When this year's marathon takes place on Monday, Biden said it would send a message "not just to the rest of the world but to the terrorists that we will never yield, we will never cower."
Braving the rain, Biden and Massachusetts Governor Deval Patrick led a flag-raising ceremony near the race finish line, where the two pressure cooker bombs exploded last year.
Biden and the crowd bowed their heads for a moment of silence before church bells tolled at 2:49pm (1849 GMT), the time when the first bomb exploded, followed by strains of bagpipes.
Just hours later, nerves were frayed when hundreds of people had to be evacuated after two unattended backpacks were found at the scene of the twin bombings.
The Boston Police Department detonated the backpacks and said a male suspect had been taken into custody.
The Boston Globe quoted Superintendent Randall Halstead saying the suspect, identified as Kevin Edson, 25, was walking barefoot, carrying a knapsack and acting strangely.
He said Edson was arrested after telling an officer he had a rice cooker in the bag, at which time the bomb squad was called in and rendered both bags safe.
Halstead did not say what police found in the bags. He said police were investigating who owned the second bag.
The attacks in the northeastern city of nearly one million were allegedly carried out by two brothers of Chechen descent who had lived in the United States for years. The brothers allegedly hid the explosive devices in backpacks.
In Washington, President Barack Obama and his staff observed a moment of silence in the Oval Office, a White House official said.
Obama said he sent thoughts and prayers to those struggling to recover, and paid tribute to the "incredible courage and leadership of so many Bostonians in the wake of unspeakable tragedy."
The two bombs sent metal fragments flying through the crowd. Several of the wounded lost their limbs.
Dzhokhar Tsarnaev, who is now 20 and his 26-year-old brother Tamerlan were identified thanks to pictures and video footage and eventually cornered by police after a four-day manhunt that paralyzed the city.
Tamerlan died after an exchange of fire with police, and Dzhokhar was wounded and captured. The younger Tsarnaev, a naturalized US citizen, will go on trial in November and could face the death penalty if convicted.
This year, organizers of the Boston Marathon -- which has been run since 1897 -- have allowed thousands more runners to register.
The number of entrants has ballooned from about 27,000 in recent years to 36,000 this year, not far off the record 38,708 who entered in 1996 in the 100th marathon.
Security has been bolstered in the wake of the attacks, with more police on the streets, a "no-bag policy", and glass bottles and large containers of any kind banned from the area.
Dzhokhar Tsarnaev has pleaded not guilty to 30 federal charges related to the bombings, including 17 serious charges that can carry sentences of death or life in prison.
The charges include using a weapon of mass destruction resulting in death, as well as conspiracy and bombing of a place of public use resulting in death, and carjacking.
Tsarnaev is also charged in connection with the fatal shooting of a campus police officer at the Massachusetts Institute of Technology during the brothers' wild getaway attempt.
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How the American's handled the Boston bombing is a good lessor for Pakistan. They pulled out all stops using every resource to hunt down the bombers until they were caught or killed - essentially closing down a major city in their efforts to eliminate these terrorist.