The home side were handed the chance to win the game in stoppage time when Luke Shaw was adjudged to have fouled Holt inside the box.
It was Norwich's first penalty of the season and Holt took responsibility from the spot only to see Artur Boruc produce a fine save to keep out his effort and deny Norwich all three points.
"It was disappointing [not to score] at that stage of the game," Hughton told Sky Sports. "It was the first penalty we have had all season. We were fortunate enough to win our last home game in the last few minutes and it would have been nice to do it today, but I think there were two fairly even teams today.
"There were minimal chances, they had a very good chance in the second half and I think Robert Snodgrass had the best chance of the game and we should have had a penalty towards the end of the first half."
Southampton were left infuriated by Norwich's late penalty, but Hughton insists there was contact made between Shaw and Holt.
"I think what Grant does, I think he gets ahead of the lad and there is contact. Whether there is enough contact to justify a penalty... but it was certainly in the box and there was some contact."
Hughton felt his side should have had a penalty at the end of the first half when Holt went down in the box again under pressure from Shaw, but referee Mark Clattenburg waved away the home side's appeals.
"I think it's easier for us to see Grant with the angles and a little more difficult for the referee and the linesman on that side, and it is a penalty and for any justification we certainly got one penalty out of today which we have deserved."
The draw leaves Norwich nine points above the drop zone on 33 points, but Hughton is unsure what will be the marker to stay up this season.
"I don't know [how many points will be needed to stay up], but the obvious one is around the 40 mark and that is depending on the results of those below you," added Hughton.
"QPR have won today and got a head of steam, Villa have won also and the teams around us are all capable of winning games and we have to make sure on the road we are capable of getting results."