The explosions came the same day that a series of apparently coordinated grenade attacks by suspected separatist rebels left a bloody trail through the streets of Srinagar, the main city in violence-wracked Indian Kashmir, killing five people and injuring 30 more.
The twin blasts at the Jama Masjid, the imposing red sandstone complex that is the heart of New Delhi's crowded old city, came about an hour before evening prayers were to be made.
"People were walking around and suddenly boom! there was a bomb," said Mohammed Salaudi, who was inside the mosque when the first explosion took place.
Salaudi said he saw at least three people with blood on their legs and torsos after the explosion, and other worshippers running in fear.
The blasts occurred within 30 minutes of each other, said K.K. Paul, New Delhi's police chief, who said they had been caused by "low intensity" improvised explosive devices.
No one has claimed responsibility for the explosions, which Sheila Dikshit, New Delhi's top elected official, said had injured 13 people.
Police put New Delhi on high alert after the explosions, stepping up security at the mosque and across the city, he said.
The first blast went off near a fountain in the mosque's central courtyard where worshippers wash their hands before offering prayers, said Syed Ahmed Bukhari, the chief cleric of the mosque. It was not immediately clear where the second explosion occurred, though officials said it was in the mosque complex.
Bukhari appealed to people to remain calm and said evening prayers would take place as usual.
The Jama Masjid is the main landmark in one of the most crowded parts of Delhi's old city, surrounded by hundreds of shops and houses lining a maze of crowded alleyways.
Less than two hours later, police reopened the mosque complex and hundreds of worshippers streamed through the main gate as night fell and the sound of prayers, said over loudspeakers, echoed across the neighborhood.
Most people stopped near the site of one blast to stare at the red sandstone flooring that covers the mosque courtyard, some of which had turned bluish-black from the blasts.
Half a dozen shoes and flip-flops, some charred from the explosion, lay scattered around, left behind as people scrambled to flee. About 30 feet away, a splotch of red had been circled in white chalk by police, with the notation "BLOOD" in large lettering.
"Who would do something like this? What sort of person is this?" wondered Mustafa Iqbal, a trader, who had come for evening prayers, as he looked at the shoes.
In Kashmir, meanwhile, a series of grenade attacks by suspected separatist rebels stunned Srinagar, the region's main city, killing five people and injuring at least 30 others, police said.
All of those killed were civilians three women and two men who died of their injuries at the city's main hospital, said Mushtaq Ahmad, a police officer.
Security forces fanned out across the city after the first blasts, stopping cars and frisking people as they rushed home.
But the explosions kept coming there had been at least eight by 8 p.m. with targets ranging from passing police patrols to the city's main bus station to a promenade frequented by tourists and lined with hotels and restaurants.
A local news agency, Current News Service said four Islamic rebel groups had separately claimed responsibility for the attacks: Jamiat-ul-Mujahedeen, Al-Mansurain, Jaish-e-Mohammad and Islamic Front.
Various Islamic militant groups have been fighting Indian security forces in the insurgency-hit state of Jammu-Kashmir since 1989 to create a separate homeland or merge the Himalayan region into Pakistan.
But even by the standards of Srinagar, a city that long ago grew accustomed to violence, it was a terrifying day.
"Everyone was frightened. By afternoon we closed down the factory for the day and all the workers went home to their families," said Amjad Khan, who owns a metal factory in Srinagar.