But the official awarded a goal kick and the visitors went on to complete a victory that took them to within three points of the Championship play-off zone, while pushing Norwich further into relegation trouble.
"I am really disappointed we didn't get anything out of this game" said Gunn.
"The lads did everything they could to get something out of the game in the second half against a very good Bristol City side but unfortunately they did not get the support they needed from the people in charge of the game.
"I have seen the incident again and there are just three people in the picture - their right-back, our left-back and the referee. How he did not give a penalty beggars belief. It was a clear barge.
"I went to speak to Mr D'Urso immediately after the game but I am a bit new to this management lark and he told me I had to wait for 30 minutes. So 30 minutes and one second later I went to see him and I didn't get much back to be honest.
"I think he knew he had made a mistake, you can tell by the look in peoples' eyes.
"It's a real shame because had we got back on level terms after 71 minutes I think the players could have gone on and won the game.
"Unfortunately that wasn't the case and all we can do now is work hard and prepare for another tough game at Preston next week.
"It's funny because I always thought Mr D'Urso was a friend of mine because he ran the line at my testimonial game and I gave him a DVD player as a gift afterwards as a way of saying thank you."
Gunn also revealed he might consider challenging the red card for Doherty just before half-time which led to the visitors going ahead from the penalty spot.
Gunn said: "It looks as though Doc got a toe on the ball as well as getting some of the player as well. We will have a close look at that one tonight and see whether it is worthwhile making an appeal."
The Robins made an impressive start to the game and it was no surprise when they took the lead on 14 minutes as Cole Skuse fired home confidently after a neat passing move down the right flank.
The Canaries hit back somewhat against the run of play 10 minutes later when on-loan defender Johnathan Grounds was on hand to prod the ball home after an effort from Carl Cort had come back off an upright.
But the visitors were not to be denied and scored what proved to be the winner from the penalty spot after Doherty had brought down Dele Adebola as the big centre-forward raced through following a poor clearance by keeper David Marshall.
Defender Bradley Orr confidently converted and the visitors held out in the second half to claim their sixth win in seven Championship games.
"We are on a very good run at the moment and it is obviously very pleasing," said Bristol City boss Gary Johnson.
"Not so long ago we were in the bottom half of the table and we are trying to make sure we did not get dragged into the relegation area. To give the boys a lift I told then we should start aiming for the play-off positions and they have responded in really good fashion.
"Now we can go into the final third of the season with a chance of pushing for a top six finish and we are all really looking forward to the challenge.
"I thought it was a fantastic Championship game with plenty of good football from both sides.
"It was very open, with play switching from end to end, and it could easily have been 7-3 to us or something like that.
"I was very impressed with the way we played early on and told the boys I was proud of them at half-time.
"There was some great passing out there, including the build-up to the first goal, and that is exactly the way I like to see us play.
"But all credit to Norwich. They had a real go at us in the second half, even though they only had 10 men."