SANTA CLARA, Calif. -- After halting practice for a second time because of a brawl Tuesday, coach Kyle Shanahan called for his team to huddle up.

He promptly delivered some choice words about what had just transpired. Underneath the anger was a simple message about how Shanahan wants his team to play.

Physical? Absolutely. Tough? Of course. Irritating? Sure.

But Shanahan wants the Niners to draw the line at throwing punches, which happened twice in that Tuesday practice -- namely between star middle linebacker Fred Warner and receiver Brandon Aiyuk.

"I want everyone challenging each other," Shanahan said Friday. "I don't care how much crap each other talks; I don't care how close they get to fighting. They can do whatever they want to get themselves to be as intense as they want and bring the best out of each other, which happens a lot that way. And it's the same on the field.

"But once you throw a punch, you get ejected or you get a penalty, and we pride ourselves on, I want people to be irritants, I want people to get as close as they can to all that stuff. I want people to get right on the line where they're about to black out, but you can't black out on the football field or you cost your team."

The problem this week for Shanahan's team was that it happened on the practice field among teammates. It was the warmest day of this camp and a longer, fully padded session, factors that multiple players said contributed to the situation. And while fights are common at every training camp, this one happened between two players expected to play significant roles this season.

The biggest fight -- between Warner and Aiyuk -- began when a late hit by Warner landed receiver Marcus Johnson in the concussion protocol.

Something had already been brewing between Warner and Aiyuk, with Aiyuk telling media a few days before, in a semi-joking way, that Warner was "annoying" and his insistence on continuing to rip at the ball and touch guys after plays ended was "irritating."

Warner countered that he believes Aiyuk is ready to take the next step in his career and he's doing what he can to help him take his game to another level.

"Specifically with Brandon, I chose him out," Warner said. "I think he's ready to make that next step into playing at an elite level. I've gotten after him a little bit ... because I know how much he has in him. And I know if I nag him a little bit, he's going to get sick and tired of that and start to hold his own. ... He's started to really gain that mindset of knowing he's a guy and he's capable. I'm trying to get the best out of him. That's it."

On Friday, Shanahan said he's fine with his players pushing one another, and he trusts them to do it the right way. But incidents like Tuesday's have to reach a natural stopping point.

"I love the intensity of it," Shanahan said. "I don't think you have to fight to be intense, though. Scuffles are scuffles but then they lead to other stuff. I think that's why we've got a guy in protocol because he took an unnecessary shot on someone which led to the big fight and then we had a bunch of haymakers and stuff thrown in there, which only break hands."

The Niners made it through the rest of Tuesday's practice and all of Wednesday's without further incident. In the interim, Shanahan has hammered home the point that his team can be physical without resorting to fights.

"I think our team is pretty tough," Shanahan said. "I think we're pretty physical. I think it most probably voted on who would be the most physical team on tape last year, I think we'd win most of that, and we didn't get in one fight last year. So, I don't think that totally pertains to toughness."