More than a dozen people were wounded in the attack in Faisal Avenue.
A passing motorcyclist was also killed in the blast.
"Now a total of four of our employees -- all sailors -- have been martyred in the attack on our bus while seven others are injured," spokesman Commander Salman Ali told AFP. Four other navy personnel died on Tuesday.
"I was trying to cross the road a few feet away from the bus when I heard an explosion and saw the bus was hit and people inside and around crying," said Asghar Ali, a passer-by being treated for injuries in hospital.
"I joined people trying to rescue the victims. There was blood inside and outside," he told AFP.
Police official Iftikhar Tarar said the blast appeared to be the work of the same group behind Tuesday's bombings, which wounded nearly 60 people and were the worst attacks on military officials in Karachi in years.
Authorities have blamed extremist organisations linked to the Taliban and al Qaeda, which was involved in the Karachi kidnap and beheading of US journalist Daniel Pearl in 2002.