Sharing a picture of the pair on Instagram, Momoa wrote they would be "reunited" for the DC blockbuster, which is due out in 2023.
The actor said they had been "busted" by a tour on the Warner Bros backlot tour, where they are reportedly filming the flick.
"Reunited Bruce and Arthur," Momoa wrote.
He said he "loved and missed" Affleck, who recently tied the knot with Jennifer Lopez, and the pair were bringing "great things" to the superhero sequel.
Affleck has played Batman numerous times in films such as Batman v Superman: Dawn of Justice (2016), Suicide Squad (2016) and Justice League (2017) — he will also appear in The Flash next year as the Caped Crusader.
The original Aquaman starred Momoa alongside actress Amber Heard. She is also expected to rejoin the cast as Mera, Aquaman's love interest, despite rumours following her infamous defamation trial loss with former partner Johnny Depp.
In June, gossip website Just Jared reported an anonymous "insider" had confirmed the actress was being recast in the sequel.
“Warner Bros decided to recast Amber Heard’s role after screen-testing the movie. They are going to be doing reshoots with Jason Momoa and Nicole Kidman,” they reportedly said.
A representative for Heard denied the reports.
“The rumour mill continues as it has from day one — inaccurate, insensitive and slightly insane," a representative told the industry publication Variety.
The story on Just Jared was later updated to say sources said Heard had "not been completely cut from the film. She still has a small role."
— PA News contributed to this report