The Egyptian MENA news agency, quoting eyewitnesses, said the explosive devices were thrown from the roof of a nearby hotel.
Blood stains could be seen in the front courtyard of the mosque, next to the famed Khan el-Khalili bazaar.
Police detonated a second device without causing any injuries.
Riot police cordoned off the area and sniffer dogs could be seen as worshippers were being evacuated from the mosque.
"I was praying and there was a big boom and people started panicking and rushing out of the mosque, then police came and sealed the main door, evacuating us out of the back," said Mohammed Abdel Azim, who was inside
the mosque at the time.
It was not clear who was behind the attack or if tourists had been deliberately targeted.
"Investigations are at a preliminary stage at the moment," Amr el-Kahky, Al Jazeera's correspondent in Cairo, said.
"It is very difficult to speculate whether foreigners were the target of this attack.
"All the Islamic groups that were operating and were violent in the nineties [in Egypt] have issued an initiative in which they declared a unilateral ceasefire against the Egyptian government."
The historic district was the scene of a previous bomb attack in 2005 in which two tourists were killed and 18 wounded.