In the three-hour episode, the pair touched on topics including vaccine conspiracies, and Hunter Biden’s laptop.
Comedian Tim Dillon was the second guest on the podcast. He, Rogan and Jones appeared in a photo that showed them failing to practise social distancing.
Both Rogan and Jones trended on Twitter as critics called out Spotify for hosting Jones via the episode when he is supposed to have been banned from the platform.
Attorney, author and activist Christine Pelosi, daughter of Nancy Pelosi, tweeted: “Alex Jones posted death threats against me. He called Sandy Hook a hoax and harassed mourning families. Now he is lying about covid vaccines. His hate speech is not just vile - it’s dangerous. WTH Spotify?”
Activist Nathan Bernard tweeted: “Joe Rogan hosted far-right conspiracy theorist Alex Jones on his podcast today. They pushed anti-vaxx conspiracies and broadcasted banned Infowars videos. Rogan continuing to platform these far-right sickos is incredibly gross and dangerous.”
Another critic said: “Joe Rogan platforming Alex Jones to millions of people a week before this election, and letting Jones propagate Joe Biden smears and pro-Trump propaganda has gotta be one of the worst things he has ever done. I've defended Rogan for a while, but this is unforgivable.”
Max Tani, a reporter at the Daily Beast, tweeted that Spotify had not responded to his question about why Jones was allowed to appear in a three-hour episode on someone else’s show.
Joe Rogan signed an exclusive deal with Spotify in May this year, which saw his podcast, The Joe Rogan Experience, removed from all other platforms.
The multi-year deal was believed to be worth $100m (£82m). Rogan’s podcast launched on Spotify on 1 September, and has since hosted guests including Kanye West and Matthew McConaughey.
The Independent has contacted Spotify for comment.