Hadi Aghily fired home from the spot before further strikes from Mehrzad Madanchi and substitute Gholamreza Rezaei secured the three points while Noh Alam Shah grabbed the only goal for the hosts.
The victory means Iran claim top spot in Group E as they have 10 points, four ahead of Thailand and Singapore with one game remaining.
"We had set the target to win the Asian Cup and we have achieved our first target of reaching it first,” said Ghotbi (pictured).
"The fans saw a fantastic match today with both teams displaying plenty of fighting spirit. I'm very proud of my team and we played in difficult circumstances.
"We started the game very well and executed our tactical plan perfectly.”
Singapore had threatened to stage something of an upset as Noh’s strike had made it 2-1 and they could consider themselves unlucky not to have equalised when substitute Khairul Amri powered his header from point-blank range onto the crossbar with the Iranian keeper Mehdi Rahmati well beaten.
"I have a lot of respect for the Singapore coach and players and they showed how far football has progressed in Asia,” added Ghotbi.
“They showed tremendous fighting spirit from the first minute to the last.
"In the end, we were the better team on the day and we showed that."
Singapore coach Radojko Avramovic felt that the initial decisions against the team left them with the proverbial mountain to climb from the start.
"The penalty was a disaster and it seemed like a handicap when those decisions went against us from the start,” he said.
"However, we did not play well and when we made the mistakes like we did, quality sides like Iran will punish us.”
Singapore travel to Jordan where a win could be enough to book their place at the AFC Asian Cup should Thailand fail to beat Iran in the other final group game in March.
“Nothing has changed in terms of our qualification,” added Avramovic.
“I had said previously that we would probably need three points from our last two games to take us to the Asian Cup. It looks like we have to get these three points in Jordan.”