Pakistan bombed the fuel depot of private airline Kam Air near Afghanistan's airport of Kandahar, the ruling Taliban said on Friday.
The overnight strikes also hit residential areas in Kabul and the eastern province of Nangarhar, killing six people, including children, and wounding more than a dozen, the Taliban said.
Government spokesperson Zabiullah Mujahid vowed that the aggression would "not go unanswered".
The strikes on the depot, which Mujahid said "supplies fuel to civilian airlines as well as to United Nations aircraft", threaten to spark further hostilities in the region.
No Pakistani airstrikes had been reported in the past week after Beijing boosted mediation efforts, including messages from President Xi Jinping to halt the fighting.
Ground clashes along the 2,600-km border had also tapered off, despite some intermittent fighting.
STRIKES TARGETED REBEL HIDEOUTS
The fighting erupted last month with Pakistani air strikes in Afghanistan that Islamabad said targeted rebel strongholds. Afghanistan called the strikes a violation of sovereignty, however, as it launched retaliatory attacks.
Pakistani security sources said the latest strikes targeted four rebel hideouts in Kabul, Kandahar and southeastern Paktia province, with one targeting an oil storage facility at the Kandahar airfield.
Afghanistan's defence ministry said it responded by launching drone strikes on a Pakistani military base in the northern city of Kohat, causing heavy damage.
Pakistan's military and information ministry did not respond to a request for comment.
Islamabad accuses Kabul of providing a safe haven to extremists launching attacks on Pakistan.
The Taliban deny the allegation, however, saying tackling extremism is Pakistan's internal problem.
Last week, the United Nations said 56 civilians have been killed in Afghanistan and 128 wounded since fighting began, displacing 115,000 from their homes. The Taliban government says more than 110 civilians have been killed.
Pakistan has rejected both tolls, saying it targets only extremists and support infrastructure.
Reuters reported on Thursday that mediation efforts by China had helped ease the fighting.
Pakistan's foreign ministry spokesperson Tahir Andrabi also said Islamabad and Beijing were engaged in a "dialogue process" on Afghanistan.
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