Brockie made it 2-0 30 seconds into the second half and looked to have completed his hat-trick shortly afterward when he volleyed the ball home only to have it ruled out for offside in a disputed call.
Chances came and went with academy player Louis Fenton again in good form, but it wasn't until stoppage time that Brockie completed the scoring from the penalty spot after Fenton had been brought down.
Herbert rang the changes again in the second half and, when the final whistle went, the Phoenix had seven under-21 players on the pitch.
"The goals keep coming for Brocks and they aren't tap-ins, either," Herbert said. "The timing of his runs is first-class and he has been assisted by some fine delivery.
"Our level was down a little with it being our third game in six days, but we managed to control the tempo of the game and kept the momentum going when needed.
"We emptied the bench again and the young players are going to benefit a lot from playing in these games. We are slowly building an understanding with the younger players at the club and need to keep working on every aspect of our game."
The Phoenix will face Shillong Lajong or URO United Sikkim in the final of the North-East Super Series on Saturday.
