The suicide bomber was apparently going towards another target when the accident took place just near the Makki Masjid in the Saddar area of the city, Additional IG Police Ghulam Qadir Thebo told reporters.
"Fortunately there have not been many casualties or injuries because the blast took place some distance from the parking plaza on an open road and it was low intensity," Thebo said.
The area was bustling with traffic at the time of the blast due to the month of Ramadan.
"Seven others have been admitted for treatment of injuries," she said.
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Thebo said the militant was riding the explosive-laden motorcycle when he accidentally collided with another motorcycle and the IED explosives went off.
Security personnel cordoned off the blast site and the Bomb Disposal Squad was called in.
A nearby building and vehicles parked in the vicinity were also damaged by the blast.
It was the first major attack since the army launched a massive operation in North Waziristan last month to flush out foreign and local terrorists.
The operation was launched after 10 terrorists stormed the old Karachi airport terminal building on June 8 in which at least 29 people were killed apart from the attackers.
A little-known Uzbekistani terrorist group affiliated with the Tehrik-e-Taliban Pakistan had claimed responsibility for the attack.