The former Brazilian midfielder's side took the lead on 49 minutes thanks to a headed goal from Ala'a Abdulzehra and the team responded by kissing the artificial turf.
Zico had criticised the surface a day earlier as being more suitable for schoolboys than World Cup qualifiers.
Iraq continued to pump high balls into their smaller opponents' box and their tactics paid off in the 85th minute when captain Younus Mahmood got a touch over the keeper's head.
Singapore, who failed to get a shot on goal in the first hour, played without any direction from the sideline as coach Raddy Avramovich was serving a one-match touchline ban for being sent off in Kunming last week.
Singapore are at the bottom of Group A while Iraq are level on points with Jordan and China who meet later on Tuesday in Amman.
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