The civil war continued in Afghanistan after the Soviet withdrawal. The Soviet Union left Afghanistan deep in winter, with intimations of panic among Kabul officials. The Afghan mujahideen were poised to attack provincial towns and cities and eventually Kabul, if necessary.

Najibullah's regime, though failing to win popular support, territory, or international recognition, was however able to remain in power until 1992. Ironically, until demoralized by the defections of its senior officers, the Afghan Army had achieved a level of performance it had never reached under direct Soviet tutelage. Kabul had achieved a stalemate that exposed the mujahideen's weaknesses, political and military. But for nearly three years, while Najibullah's government successfully defended itself against mujahideen attacks, factions within the government had also developed connections with its opponents.

According to Russian publicist Andrey Karaulov, the main trigger for Najibullah losing power was Russia's refusal to sell oil products to Afghanistan in 1992 for political reasons (the new Yeltsin government did not want to support the former communists), which effectively triggered an embargo. The defection of General Abdul Rashid Dostam and his Uzbek militia, in March 1992, further undermined Najibullah's control of the state. In April, Najibullah and his communist government fell to the mujahideen, who replaced Najibullah with a new governing council for the country.