Kelly also doused speculation the 49ers were planning to cut Hayne, which led to the Australian making a face-saving exit.
The 49ers instead were bullish on Hayne, praising his ability to pick up Kelly's new offence and excited about using his powerful, 188cm body and skills.
"He's a really sharp learner," Kelly told reporters on Tuesday at the 49ers' Santa Clara facility.
"We were excited. He's a big body and has a skill set."