Chose to fight Blue at Battle Tree, how do I get Kanto Starter Mega Stones?

In Pokemon Sun and Moon, once you enter the Battle Tree for the first time, you get challenged by Red and Blue, the "Champions" of Kanto. The Mega Stones for the Kanto starters are given by Red, but I chose to fight Blue at the Battle tree, who did not give me the Venusaurite, Charizardite X/Y, and Blastoisinite.

After choosing the trainer to fight, both trainers left and I did not receive the Mega Stones for Venusaur, Charizard, and Blastoise. Is there another chance for me to obtain the stones?

Solution 1:

In regular singles you have to fight Red on the last battle (20) and then he will appear outside of the Battle Tree and give you the stones. He doesn't give out stones on Super Singles.

Solution 2:

According to Serebii, you are able to fight Red (and Blue, for that matter) in the Battle Tree randomly. They are listed as Special Trainers and you will fight one of them every 10 battles in Super Battles.

In the Super Battles, these trainers will come every 10 wins in a streak and offer a bit of a challenge.

Since defeating Red is what nets you the Venusaurite, Charizardite X/Y, and Blastoisite, it appears that regardless of whether or not you choose to defeat Red at the entrance of the Battle Tree, you will just have to beat him when he appears during your Battle Tree challenge as the last battle in Regular Singles, as mentioned in Alexander's answer.

Besides Red and Blue, you can also end up fighting Anabel, Colress, Cynthia, Dexio, Grimsley, Guzma, Kiawe, Mallow, Plumeria, Sina, or Wally.