In June 1993, an unsuccessful government attempt to disarm mutinous paramilitary forces precipitated the fall of Azerbaijan's fourth government since independence and provided the opportunity for Aliyev's return to power. The erstwhile communist's reappearance was part of a trend in which members of the former elites in various parts of the old Soviet sphere reclaimed authority. Suret Huseynov, a one-time troop commander in Nagorno-Karabakh dismissed by Elchibey, led the paramilitary forces that triggered the president's removal. In support of one of Elchibey's rivals, Huseynov had amassed troops and weaponry (largely obtained from the departing Russian military) in his home territory. He then easily defeated army forces sent to defeat him and precipitated a government crisis by marching toward Baku with several thousand troops.

Huseynov's exploits thoroughly discredited the Elchibey APF government in the minds of most Azerbaijanis. After several top government officials were fired or resigned and massed demonstrators demanded a change in government, Elchibey endorsed Aliyev's election as chairman of the Melli-Majlis. After a brief attempt to retain the presidency, Elchibey fled Baku in mid-June as Huseynov's forces approached.

Aliyev announced his immediate assumption of power as acting head of state, and within a week a bare quorum of Melli-Majlis legislators, mostly former communist deputies, formally transferred Elchibey's powers to Aliyev until a new president could be elected. Aliyev then replaced Elchibey's ministers and other officials with his own appointees. Huseynov received the post of prime minister. The legislature also granted Huseynov control over the "power" ministries of defense, internal affairs, and security.

In late July 1993, Aliyev convinced the legislature to hold a popular vote of confidence on Elchibey's moribund presidency and an extension of a state of emergency that had existed since April 1993 because of military setbacks. Although the APF boycotted the referendum, more than 90 percent of the electorate reportedly turned out to cast a 97 percent vote of no-confidence in Elchibey's rule. This outcome buttressed Aliyev's position and opened the way for new presidential elections.

In early September 1993, the Melli-Majlis scheduled new presidential elections for October 3, 1993. Removal of the maximum age requirement in the election law allowed Aliyev to run. Aliyev's position was strengthened further in August when paramilitary forces defeated a rebel warlord who had seized several areas of southern Azerbaijan and declared an autonomous republic of Talysh-Mugan.

Early in his tenure as acting president, Aliyev stated that his political goals were to prevent civil war, regain territory lost to Armenia during the Nagorno-Karabakh conflict, and ensure the territorial integrity of Azerbaijan. Aliyev claimed that freedom of speech and human rights would be respected in Azerbaijan, although he also called for continuing a state of emergency that would ban political rallies. Huseynov had stated in June that the Azerbaijani government woul22e uld pursue a negotiated settlement in Nagorno-Karabakh, but, if that failed, a military victory was the goal. He added that the government focus would be on improving the Azerbaijani armed forces, stabilizing the economy, and securing food for the population.

Data as of March 1994