Mohammad Nouri, who replaced Mojtaba Jabbari in the second half, scored the winner for Iran 8 minutes from time at Tehran's Azadi Stadium, which saw an attendance of about 10,000.
Osasuna's Javad Nekounam and Masoud Shojaei, Bochum's Vahid Hashemian and Fulham's Andranik Teymourian, who did not take part in Wednesday's action, will join Ali Daei's squad next week.
Association of Football Federations of Azerbaijan (AFFA) had filed an official complaint to FIFA with respect to a decision by Iran Football Federation (IFF) to appoint an Iranian referee for the match. Hedayat Mombeini, however, refereed the game as scheduled.
The Iranian squad will hold a training camp in the southern island of Kish before heading to Jeddah for the September 6 match against Saudi Arabia.
Iran has been drawn in Group B of the 2010 World Cup qualifiers along with Saudi Arabia, South Korea, the UAE and North Korea.
Azerbaijan, with German coach Berti Vogts who was appointed in April 2008, will face Wales and Liechtenstein on September 6 and 10 in its first two World Cup qualifiers. Azerbaijan was placed 138th in the latest FIFA ranking.
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