The ACB said in a social media post on Saturday that the cricketers were "targeted during a gathering" in Urgun district on Friday when they returned home after playing a friendly match in Sharana, the capital of Paktika province.
ACB spokesman Said Nasim Sadat identified the players as Kabeer Agha Argon, Sibghatullah Zirok and Haroon, who, like many Afghans, goes by only one name.
"The ACB considers this a great loss for Afghanistan's sports community, its athletes and the cricketing family," the ACB said.
"In response of this tragic incident and as a gesture of respect to the victims, the Afghanistan Cricket Board has decided to withdraw from participating in the upcoming Tri-Nation T20I Series."
Afghan captain Rashid Khan and the Afghanistan Sports Journalists Federation welcomed the decision. The federation condemned the strike as a "barbaric and shameful act, which stands in clear violation of all international laws".
The tri-series, also featuring Sri Lanka, was to be played between November 17 and 29 in Rawalpindi and Lahore as part of the teams' preparations for next year's T20 World Cup in India and Sri Lanka.
It would have been the second tri-series featuring Pakistan and Afghanistan in four months after both teams competed in a three-nation tournament in the United Arab Emirates in September. Pakistan beat Afghanistan in the final of that tournament.
