Davis angrily confronted Crabtree during Wednesday's practice, and coach Mike Singletary had to step between them.
"It was a matter of being a team captain. All I was doing was taking care of my responsibilities and doing my job," Davis said after Thursday night's 17-14 preseason win over the San Diego Chargers.
"I was just expressing the way I felt at the moment. I just pretty much said whatever was on my mind at the time. Just pretty much giving him a check, getting his head leveled and just getting on him about some things he did in the past."
Singletary and the two players headed to the locker room to chat for about 10 minutes. Each returned to practice, but separately. Neither Crabtree nor Davis played at all this preseason for the Niners (4-0) because of injuries.
Davis said his issue with Crabtree was football related but not about the second-year wideout not playing during the exhibition schedule. Crabtree left without facing reporters after the game and hasn't spoken formally since the start of training camp Aug. 1. He has long had the reputation of being a diva.
"I hope he got the message. I think he did, I strongly believe, but if anything I see that I feel is wrong or that needs to be addressed, then I'm going to say something," Davis said. "I don't really have any frustrations with Michael. He just did some things during that time that I didn't like. That's all. ... It was basically taking ownership."
Crabtree, the Niners' 10th overall pick in the 2009 draft out of Texas Tech, finally ended a 71-day contract stalemate last October. By Oct. 25 at Houston, he had cracked the starting lineup.
Davis said he no longer has a problem with Crabtree. The 49ers are counting on both men to be two of their biggest offensive stars.
"We're great. I love him like a brother. I'll take him to Smoothie King tomorrow," Davis said. "I feel like everybody's on the same page. We still have some growing to do. We have Week 1 coming up, and that's all we can concentrate on at the moment. We don't need any distractions."
The 49ers went 8-8 last season and are trying to end a seven-year postseason drought. Davis is coming off a career year in which he made his first Pro Bowl after tying Antonio Gates' NFL record for touchdowns by a tight end with 13.
While Crabtree had been nursing a neck injury, he hasn't been limited in practice. Singletary said he opted not to play Crabtree in Thursday's exhibition finale on a night when many of the offensive starters were held out.
"I just feel when you take a step back and look at it our whole offense wasn't going to be in there anyway," Singletary said. "Let's start on the same page next week."