"The incident occurred near Ayesha Manzil in Federal B Area where the miscreants threw the hand grenade from an overhead bridge near the Imambargah," a police official said.
"The grenade was apparently thrown at a police mobile outside the Imambargah but it landed inside the compound of the building," he said.
The incident caused panic in the area where major Shia Muslim religious gatherings take place during the first 10 days of Muharram.
There is a heightened security alert in Karachi during the month of Ramzan because of sectarian attacks on Shias in the past by banned Sunni sectarian outfits.