"We definitely will retaliate," the general said, in comments reported by state media.
Mr Jafari was speaking at one of two funeral ceremonies held on Friday for the attack's victims.
The Jaish al-Adl Sunni militant group claimed responsibility for the bombing, which wounded 12 people.
The attack took place in a southeastern region near the village of Chanali, where security forces are facing a rising number of attacks from the militants, who mainly operate near Iran's border with Pakistan.
The region is known as a crossroads for narcotics trafficking gangs and jihadi networks sometimes rooted in local tribes.
On Saturday, Iran said Pakistan should crack down on the groups or to face the possibility of military action from Tehran.
"If Pakistan does not carry out its responsibilities, Iran reserves the right to confront threats on its borders ... based on international law and will retaliate to punish the terrorists," said Mr Jafari, according to state news.
Officials have repeatedly called on the neighbouring country to take action against the Jaish al-Adl and similar groups.
Additional reporting by agencies