Captain Javad Nekounam scored the winner at the Azadi Stadium with a 72nd minute header from a left-wing Andranik Teymourian cross and much to Ghotbi's relief following an unsatisfactory opening period.
"I was very unhappy with the first-half," he said.
"Jordan played defensively, closed the game down and we played with no pace. But we had much more energy in the second-half and we improved our quality. We created good chances and scored a good goal.
"This goal showed that we have a good leader like Javad Nekounam who can change the destiny of a match at any moment.
"We have to accept that the time when we beat teams three or four-nil has changed and teams like Jordan have improved.”
Fewer than 20,000 fans turned up to watch Iran at the Azadi Stadium, a sign of continued unhappiness with the national team following its failure to qualify for the 2010 FIFA World Cup.
"I said before that every game is a small step forward because we need to change our football," Ghotbi added after thanking the fans who turned up to watch the game.
"I just hope people have more patience with us and give the younger players a chance and put less pressure on them so that we can have a good national team in the future.
"If you have patience, I'm sure you'll be proud of this team."
Meanwhile, Jordan coach Adnan Hamad underlined he still has hopes of qualifying for Qatar in 2011 despite the fact his side remain rooted to the bottom of the group on one point.
"We still have three matches (left) and we're hope to get at least seven points and qualify," said the Iraqi, who was named Asian Coach of the Year in 2004.
"If we could have taken a point from Tehran it would have been a good result but that didn't happen.
Jordan's cause wasn't helped when veteran striker Mahmoud Shelbaieh was sent off for a second yellow card a minute after Iran's goal.
That incident sparked a series of strong challenges from the visitors, with striker Amer Deeb kicking out at the bench when he was substituted.
"Our players were angry because they started the match with confidence but when we conceded, they suffered psychologically and became aggressive," added Hamad.
"We have to get ready for the next match. Every match has its own story and we have to forget today and play to win (in Amman)."