Police said three people were wounded in port city of Karachi but bomber and accomplice died.
The van was heading to an industrial area where the five Japanese nationals work at Pakistan Suzuki Motors, according to local police chief Arshad Awan.
The Japanese nationals escaped unhurt on Friday, Aswan said, adding that the three people wounded were in stable condition in hospital.
Two security guards were travelling in the bullet-proof van after receiving reports about possible attacks on foreigners working in Pakistan on various Chinese-funded and other projects.
Police said a suicide bomber on a motorcycle set off his vest, while another assailant was shot dead by police patrolling the area.
Tariq Mastoi, a senior police officer, said the quick police response foiled the attack.
There was no immediate claim of responsibility for the assault in Karachi, the country’s largest city and the capital of the southern province of Sindh.
Pakistan’s President Asif Ali Zardari and Prime Minister Shehbaz Sharif denounced the attack on the Japanese workers.
Armed groups have in the past targeted Chinese nationals working in Pakistan on projects relating to the China-Pakistan Economic Corridor (CPEC). China is one of Pakistan’s closest allies and has invested $62bn in the CPEC infrastructure project that spans a series of highways linking southwestern China to Gwadar port on the Arabian Sea.
In March, five Chinese and their Pakistani driver were killed when a suicide attacker rammed his explosive-laden car into their convoy near Besham city in the northwestern province of Khyber Pakhtunkhwa. They were on their way from Islamabad to Dasu, the site of a hydroelectric dam being constructed by a Chinese company, about 270km (167 miles) from the capital.