Herbert gave his team a rev up at halftime, as well as replacing Benji Totori with Fenton and Tom Doyle with Cameron Lindsay, and they looked a different team.
Completely over-running Shillong, the Phoenix created chances galore but could only manage a Paul Ifill penalty on the scoreboard which levelled the score at 2-2.
In contrast Shillong had only one shot at goal in the second half, and what a strike it was with diminutive winger lashing the ball into the top corner of the net from all of 30 metres seven minutes from full time.
While disappointed by the loss Herbert was happy overall with the tour.
"We got a good workout today, especially in the first half, which was what we needed," Herbert said.
"It has been a tough trip but we got four good games under our belt and finished the tour with no injuries.
"Louis (Fenton) was really impressive today and I would have to say he has been the player of the tour overall."
Captain Andrew Durante agreed it had been a difficult trip but said it was good to get away from the training ground and playing some meaningful games.
The Phoenix leave Shillong early tomorrow morning and arrive back in Wellington, minus Herbert and six All Whites and Solomon Islands representative Benji Totori, on Tuesday afternoon.