After the meeting with ambassador Shafkat Saeed, the two countries resolved to form a committee to improve security over their shared borders, foreign ministry spokesman Mohammad Ali Hosseini said according to the state-run IRNA news agency.
"The Pakistani ambassador was summoned to the foreign ministry to give explanations. Discussions were undertaken and a committee was formed between the two countries to reinforce border security."
A car bomb attack in Zahedan, a city 40 kilometres (25 miles) from the Pakistan border, on Wednesday killed 11 Revolutionary Guards, followed by late night clashes and a percussion bomb on Friday which lightly wounded one person.
"The investigation and the confessions show that foreigners are implicated in these actions," Hosseini added, without specifying further.
Local officials said the unrest bore suspicious hallmarks of involvement by the United States and Britain, reiterating previous allegations of Western trouble-making in the southeastern Sistuan-Baluchestan province.
According to unconfirmed website reports, Wednesday's attack was claimed by a shadowy Sunni militant group, Jundallah, which has been blamed for a string of armed incidents in the volatile province.
Zahedan, a dusty and tense border city, is the capital of Sistan-Baluchestan province which borders both Afghanistan and Pakistan and has been the centre of low-level unrest over the past months.
It has a substantial Baluch community, a minority Sunni Muslim group.