Saints striker Manolo Gabbiadini thought he had given his side the lead early on at Wembley Stadium when tapping home from a Cedric Soares cross, only for the officials to rule out the goal for an offside infringement.
The contentious call was made due to Ryan Bertrand being ahead of the ball when it came into the box, but he was not directly involved in play at the far post and Italian poacher Gabbiadini - who went on to score two legitimate goals in the 3-2 thriller - was stood onside.
Puel believes that there is a simple way to stop a similar error from being made in the future, though he also accepted that no complaints can be made on this occasion.
"We scored first, the decision was not for us. I'm proud of my players for a fantastic game," he told reporters. "It's a big disappointment of course with today, with the quality of the game. I'm proud of course of my players.
"Perhaps [the disallowed was a turning point], it's always better to go 1-0 up. I would like of course the video for the future, for this situation for example.
"But for the moment football is without video, and sometimes a bad decision arrives against us or another team, it's important to accept this. But I am also disappointed for the players, for the fans. I would like to say that for the fans, because we had the support today in the game."
Gabbiadini is the fourth Italian player to score in the League Cup final and just the second player to do so twice against Manchester United after Dean Saunders.