"I stabbed one in the leg, I think, with my pen," he said on the 911 call to police in Dayton, about 60 miles north of Cincinnati.
Police said Tuesday no one was on the bus at the time.
Wagoner said in the 911 call that he felt two shots to his chest, but he didn't think the bullets got through the booklet in his shirt pocket. Police said in their report that two small-caliber bullets hit the booklet called "The Message," which has Bible verses in contemporary language and were found lodged inside the book.
"It just feels like I've been hit with a sledgehammer," Wagoner said. "I've got a book in my pocket, and I don't think they made it through this book."
Wagoner told police he just started carrying the book about a week ago.
Miami Valley Hospital in Dayton confirmed Tuesday that Wagoner remained in the hospital, but the hospital would provide no other information. The authority said in a statement that Wagoner was recovering and doing well.
The initial police report said Wagoner stopped his bus to check a possible mechanical problem. The report also said Wagoner told officers that when the three men approached him, he heard one say: "If you want to be all the way in the club, you have to kill the polar bear."
He told police he grabbed the gun when he was shot in the chest and began struggling with the suspect. He said he was shot again in the leg and began choking the suspect. One of the other men kicked Wagoner in the side, and the bus driver said he was punched several times in the face, according to the police report.
Wagoner said the third man then pulled a knife, stabbing him in the arm as he tried to block the knife.
The bus driver said he then pulled a pen from his pocket, stabbing the suspect.
Police described the aluminum pen as about 6 inches long and wider than normal. It was described as a "self-defense pen" that Wagoner said he always carries.
He told police that in firing on the suspects, he may have struck one of them.
"Amazingly, his injuries are not life-threatening," Dayton Police Sgt. Michael Pauley told the Dayton Daily News.
Associated Press Writer Dan Sewell contributed to this report.