كتب : Amro Hassan
Deco put Portugal ahead three minutes after the hour mark and Cristiano Ronaldo sealed the victory ten minutes from time.
Portugal now top Group D with six points while Iran were sent packing after remaining pointless in two games.
Coach Luiz Felipe Scolari made some changes in Portugal's starting line-up, with Maniche, Costinha and Deco all in the starting line up.
Deco, who missed Portugal's opener with injury, had an immediate impact and almost put Portugal ahead in the 13th minute after he took down Luis Figo's cross before hitting a left-footed volley that was tipped over the bar.
Portugal came close to breaking the deadlock in the 33rd minute when Cristiano Ronaldo headed Figo's corner towards the net but Hossein Kaabi cleared the ball just before passing the line.
Miguel had a chance to open the score line just before the interval when he received Maniche's chip in the box and fired from a tight angle but the ball went just inches wide.
kicking-off the second period in a more attacking style, Ronaldo darted into Iran box and fired a vicious shot only to produce a great save by Iran goalie Ebrahim Mirzapour.
The Portuguese managed to find the net in the 63rd minute when Deco marked his return with a fabulous strike from the edge of the box after a quick exchange with Luis Figo.
Substitute Rasoul Khatibi missed a golden opportunity to equalize in the 69th minute when he was released with a long pass but he waited too much time before sending a weak finish wide.
In the 78th Ricardo had to stretch wide to save Hashemian's header and from the resulting counter, Luis Figo won a penalty-kick for Portugal.
The Inter winger rounded Yahya Golmohammadi who had to bring him down in the box. Ronaldo stepped-up and hammered the resulted spot kick into the top corner.
After the second goal, Iran totally collapsed and Pedro Pauleta had two late chances to add a third for Portugal but Mirzapour was in the rescue for Iran.