In addition to Uji Shrine another shrine seen in Sound! Euphonium is Agata Shrine. The closest train station is JR Uji Station.
Image from S1E8 - 15m20s
Shrine torii gate.
The main shrine building.
Image from S1E8 - 15m23s
View towards the shrine grounds from the main building.
Image from S1E8 - 15m47s
Closeup of the main building.
This location was visited on 2015/11/05.
Agata Shrine official website
Special thanks to the ones who went here before: