Man of the match Hadi Aqili scored a pair of almost identical headers in the 36th and 38th minutes to give Afshin Qotbi's team a two-goal lead in the first half.
Mehrdad Oladi sealed the victory when he scored from close range four minutes into the second half at Amman's King Abdullah Stadium.
“The WAFF championship is a good opportunity for us to get ready for the 2011 AFC Asian Cup,” Qotbi said after the match.
In the other match of the opening day, Jordan and Syria drew 1-1. The hosts took the lead through a goal by Abdullah Khaled Dib in the 13th minute, but Mohamed Zino restored parity for Syria six minutes from time and the score stayed that way until the final whistle.
The Iranian team is scheduled to face Oman on Tuesday in its second group match.
Iran won the title in 2000, 2004, 2007 and 2008 while Iraq claimed the title in 2002.
The tournament ends on October 3.