SANTA CLARA — We have a leader in the clubhouse for the 49ers’ long, drawn out quarterback competition.

Blaine Gabbert took every first-team rep in Friday’s joint practice with the Texans, and for the most part, he torched Houston’s secondary.

The 26-year-old excelled in an 11-on-11 red-zone portion of practice, throwing back-to-back touchdowns to both Bruce Ellington and Garrett Celek. Later, during a hurry-up portion, Gabbert connected on a 35-yard stop-and-go route to Jerome Simpson, who raced down the sidelines for further yardage.

On a day where scrutiny from the coaching staff and media would reach its climax, it was arguably Gabbert’s best performance in training camp.

This is the first time all summer Gabbert has received every first team rep. It was clear he was building a rhythm, and he could privately make the case to Chip Kelly that he’s a better quarterback when he doesn’t have to split time with Colin Kaepernick.

“That’s how I approach every day — like I’m the starter,” Gabbert said. “Let the decision be made for itself. I’m just going to go control what I can control and go sling the rock and put some points on the board.”

Kaepernick’s arm fatigue in his throwing shoulder came at the worst time possible. It was the second consecutive day the 28-year-old was unable to throw a football.

Are the 49ers partially at fault for the injury? Kelly said each quarterback is throwing between 86 and 102 passes per day in training camp, a workload Kaepernick admitted is much larger than his recovering body is used to. Kaepernick underwent surgeries on his shoulder, thumb and knee in the offseason.

In hindsight, the team probably should’ve given Kaepernick a day or two of rest in camp. Given how poorly Houston’s secondary played, this could’ve been his chance to show the coaching staff he’s conquered some of the demons that have plagued him in the pocket.

But Kaepernick would not concede that this quarterback competition is over. He has hopes to play Sunday in the preseason opener, and told the media Kelly’s indicated he will give him a chance to start a preseason game.

“I would to have loved to get those reps, but it’s also something that we’re in preseason practice. We don’t play a game for about another month. So we want to make sure we stay ahead of this before we get to the season.”

With a strong showing Sunday against the Texans, there is a chance Gabbert could win the quarterback competition before the Niners’ second preseason game against the Broncos. But Kelly still wanted to pump the brakes on that assumption, even if players like Torrey Smith have said they want this decision made sooner rather than later.

“I don’t want anybody on our staff to make the wrong decision on who our quarterback to be just because we said, ‘Why did we do it? Because we wanted to name him by a certain date,’” Kelly said. “You know, I want to make sure we have the right quarterback to lead the San Francisco 49ers this year.”