The Kabul match, set for July or August, would have been followed by a fixture in Pakistan and a full series at an unspecified date.
But the Afghanistan Cricket Board issued a strongly worded statement late on Wednesday, cancelling the matches in light of a truck bombing in the city's diplomatic quarter that killed at least 90 people.
No group has claimed responsibility for Wednesday's attack, although the Taliban has denied involvement.
"The ACB hereby cancel all kinds of cricket matches and initial mutual relationship agreement with the Pakistan Cricket Board," the Afghan board said on its Facebook page.
"No agreement of friendly matches and mutual relationship agreement is possible with a country where terrorists are housed and provided safe havens."
Afghanistan's intelligence agency has blamed the Taliban-allied Haqqani Network for the attack, which has been linked to Pakistan's military in the past.
The development leaves Pakistan's cricketers even more isolated in the region.
India has refused to play a full series since the 2008 Mumbai attacks, while ties with fellow Test team Bangladesh have also soured after Pakistan pulled out of a planned series in July.
Pakistani officials said they were unhappy that Bangladesh were not willing to send their team to Pakistan.
Only minnows Zimbabwe have been willing to tour the insecurity-wracked country since a 2009 militant attack on the visiting Sri Lanka team.
Cricketing relations between Afghanistan and Pakistan were not always so frosty.
Afghans learned to play cricket in refugee camps in Pakistan after they were forced to leave their homes in the wake of the Soviet invasion in 1979.
The sport struggled to get a foothold in Afghanistan under the hardline Taliban, but has become hugely popular since the Islamist regime was toppled in a US-led invasion in 2001.
While Pakistan has supported the Afghan team by supplying equipment and arranging fixtures with the fledgling side, rival India has also been keen to lend its support.
Last year, Afghanistan's national team shifted its base from Sharjah in the United Arab Emirates to Noida, Delhi, while India's former batsman Lalchand Rajput replaced Pakistan's Inzamam-ul-Haq as their national team coach.