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The 49ers reduced their squad size to 75 with 10 players copping the boot on Tuesday (AEST).
Hayne must now survive one more cut on Sunday (AEST) to make the 49ers final 53-man squad for the upcoming NFL season.
After performing strongly in the 49ers' three pre-season games against Houston, Dallas and Denver, Hayne is odds-on favourite to make the final roster with coach Jim Tomsula praising the 27-year-old.
"I feel very good about his abilities to field. I feel very good about his abilities to perform with a ball in his hands on special teams," Tomsula said.
"The coverage parts of it? I’ve seen a lot of improvement there. The guy will fly down the field in those areas.
"So, all of those things I’ve seen what I need to see. I think it’s been a great evaluation on him."
Among the players waived in the first cut was Hayne's fellow cross-sport athlete Lawrence Okoye - a British former Olympic discus thrower.
The other hopefuls cut were: Steve Beauharnals (LB), Corey Acosta (K), Sean Hooey (T), Mylan Hicks (CB), Mario Hull (WR), Nigel King (WR), Chuck Jacobs (WR), Trey Millard (FB) and Shawn Lemon (LB).