The missiles targeted a Hamas leader in the Shijaiya district late on Sunday as he stood with a friend near a local mosque, witnesses told Aljazeera.
Medics at Shifa Hospital said the two men were in serious condition undergoing surgery.
The third person injured was a woman with no connection to the resistance movement.
The Israeli army has declined to comment.
The raid came as occupation forces pursued a separate offensive in northern Gaza to stop homemade rocket attacks on Israeli towns and illegal settlements.
Sixty-six Palestinians and three Israelis have died in the five-day raid.