Sussex Police has launched an investigation into the alleged abuse, which has been condemned by Wolves.
The incident came on the weekend the Premier League dedicated to supporting the Rainbow Laces campaign which promotes LGBT inclusion in sport.
Rainbow coloured flags and banners were on show as the two teams came onto the field at Brighton's Amex Stadium, while the home supporters held coloured cards aloft.
Clubs and players across the Premier League backed the campaign over the weekend.
The Sussex force confirmed two men had been arrested following reports of homophobic gestures during the 2-2 draw and that they had been released as the investigation continues.
A spokesman said: "Two football fans were arrested following reports of homophobic gestures made at the Amex Stadium on Sunday, December 8.
"The suspects – both away fans during Brighton and Hove Albion’s match against Wolverhampton Wanderers – were identified by club stewards and arrested on suspicion of using threatening or abusive words or behaviour likely to cause harassment, alarm or distress.
"The two men – aged 46 and 48, and both from Bridgnorth in Shropshire – have been released under investigation pending further inquiries."
Wolves said in a statement: "Wolves can confirm that there were two arrests for homophobic abuse at yesterday’s game against Brighton & Hove Albion.
"There is no room in football or society for discrimination of any kind, and the club strongly condemns such behaviour.
"Our ethos at Wolves is about being ‘One Pack’ - an attitude our supporters are very passionate about and that extends to our relationships across the football community, regardless of rivalries on the pitch.
"The club is now offering its support to Sussex Police in what is a criminal investigation."
It was another incident which marred the weekend's action after a Manchester City supporter was arrested for alleged racist abuse during the derby with Manchester United.
Everton are also investigating reports of homophobic chanting during their game with Chelsea.