Leeds Contemporary Singers - made up of second and third year music students and their lecturer Craig - beat Liverpool based The LMA Choir in the final battle of Saturday night's show.
After four other choirs were eliminated in a series of rounds, the remaining two groups took it in turns to perform guest judge Will Young's Evergreen before the former Pop Idol singer joined Leeds Contemporary Singers, indicating they had won the episode.
The winning group said: "We don't know what to say. We are never lost for words and don't know what to say but thanks to everyone, thanks."
Young said: "It was so hard to choose a winner but I am really thrilled. It was a pleasure to sing with them for 10 seconds so we could do it again in the final, but well done to both groups."
Judge Kelis said: "I'm so excited to see what the guys come up with for the final. I think the combination of Will and this group will be explosive."
Fellow judge Gareth Malone added: "Both groups were absolutely fantastic. It was a very very good performance tonight."
The LMA Choir still have a chance of reaching next month's grand final as the judges will offer one of the runners-up a wild card entry.
The show received a mixed reception on Twitter, with one fan calling it "another failed attempt" at creating a real-life version of hit a cappella movie Pitch Perfect.
@Tinee84 added: "bit cringey cos of Mel. Puns work for GBBO but not here. Is it an a capella comp or choir? And why is the riff off prepped?"
Louise Emerson (@Lushleys) also gave it the thumbs down, writing it was "going on far too long".
Paula McAleer (@PaulaMcaleer) wrote: "#PitchBattle mic drop. Omg. Best show EVER" while Justina Jordan (@JusTeasyJ) tweeted: "Pitch battle was AMAZING well done to theLeeds group for winning. It was a close call."
Pitch Battle returns on Saturday June 24 at 7.30pm on BBC One.