Pakistani officials said Iran fired six mortar shells, which landed near the border town of Mashkail. Pakistan is then thought to have fired back.
The two countries share a long desert border which straddles Balochistan province in south-west Pakistan and Sistan Baluchistan in eastern Iran.
Last week, Pakistan said a soldier died and three were hurt by Iranian guards.
Pakistan has been accused by predominantly Shia Muslim Iran of failing to stop cross-border attacks on its forces by extremist Sunni Muslim militants.
Sistan Baluchistan, which also borders Afghanistan, has been the scene of frequent clashes in recent years between Iranian security forces and drug-smugglers and Sunni rebel groups.
This escalation comes at a time when Pakistan is already facing tensions with India on its eastern border.
At least 17 people have died and dozens have been wounded this month as Pakistani and Indian forces traded fire on both sides of the Kashmir frontier.
But the tensions with Iran prompted Pakistan to hold a meeting in Tehran to boost intelligence co-operation, Pakistani media reports say.
Earlier this year the abduction of four Iranian soldiers also heightened regional and sectarian tensions. The guards were taken into Pakistan by Sunni militants but eventually released.