City, who face Chelsea in the European showpiece a week on Saturday, blew a two-goal advantage to lose 3-2 on a raucous evening on the south coast.
Almost 8,000 jubilant Albion followers were treated to an unforgettable occasion at the Amex Stadium as second-half finishes from Leandro Trossard, Adam Webster and Dan Burn completed a sensational turnaround.
Despite having Joao Cancelo sent off just 10 minutes in, the visitors led 2-0 thanks to an Ilkay Gundogan header and a superb Phil Foden goal, prior to their unexpected capitulation.
But after the final whistle the City bench, including Guradiola, were furious with Albion's head coach after his celebration following Trossard's second half goal that hauled Albion back in the game at 2-1.
"The first goal I was a bit emotional," said Potter.
"It was not my finest hour and I have to apologise for that. It was not done with any intent towards anybody, it was an emotional response from me but it was not a good one.
"I apologise to them and no offence was meant but I understand from their perspective that it was not a nice moment."
Guardiola had previously spoken about Potter in glowing terms and after their last encounter he praised Potter as England's finest coach.
The City boss had no such compliments for his opposite number this time. "It will be said personally, not here," bristled the Spaniard when asked for his take on the incident.
Potter though was delighted with the victory that saw Brighton equal their record Premier League points tally with 41. Burn netted the winner with his first ever goal for the club.
"I don't rule anything out with Dan to be honest," said Potter. "He is that type of character, that type of player. I am so pleased for him.
"I have spoke about him before many times about his attitude and professionalism and what he gives to the team is so important.
"Sometimes people don't see it but he is such an important player for us in the dressing room and as a person.
"Nice for him to get that goal. I couldn't really see how it finished up but it was nice to see it hit the back of the net."