Herbert is the longest serving A-League coach and has managed the Phoenix for more than 150 games since the club's inception in 2007. He was also in charge of the New Zealand Knights for their last five games.
His contract was due to expire at the end of the season before a two-year option on "ootball-related matters'' was meant to kick in.
Herbert will still be in charge of the All Whites, who are on the verge of progressing to an intercontinental playoff match against the fourth-placed side from North and Central America for a spot at next year's World Cup, and he cited this as a reason for his resignation.
"The results this year have not been what anyone would have wanted and I felt that it was time for someone else to take a fresh look at things at the club,'' Herbert said in a statement. "The coaching staff and players have all put in a huge effort this year but we haven't got the results we wanted.
"So with the need for a fresh look, along with the fact that this year is an extremely important one for the All Whites, I felt I needed to step down as the Phoenix head coach. I've had a long and very successful tenure at the club and will always be proud of what I have achieved. But all good things must come to an end and it's time for new coaching blood and for me to move on to new and exciting challenges.''
It's still not clear what the job of a technical advisor to the board would entail and how much time this would take up.
In January, Phoenix co-owner Gareth Morgan gave him a vote of confidence and said a possible role as director of football would suit Herbert in the future but the club have since backed away from having a director of football.
Chairman Rob Morrison also said Herbert's position would be reviewed at the end of the season. Morrison said today the club didn't want to lose Herbert so offered him the role as technical advisor.
"While the board accepted Ricki's resignation, we were keen to ensure that his knowledge and expertise was not lost to the club,'' Morrison said in a statement. "Ricki has an unparalleled record in the Hyundai A-League. Without his contribution, the Phoenix could not have had the success it has had.
"We are very pleased that Ricki has agreed to accept the advisory role to the board.''
Phoenix captain Andrew Durante and Greenacre are due to front media after training later this morning. It's understood Durante found out about Herbert's resignation on radio this morning.