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Herbert's position had been under threat for some time as the Phoenix languish in last on the A-League table and his move to resign was probably done before the club took action.
They have won only five of 22 games this season - only one in 2013 - with only five games remaining in the regular season. They have also been outscored 23-7 over the last nine matches.
Wellington are the only club to reach the playoffs in each of the last three years in the generous system that sees six of the 10 teams qualify and, quite incredibly, still have a slim chance of making the playoffs.
Assistant coach Chris Greenacre will take charge of the side for tomorrow's visit of Newcastle and is expected to remain in the job for the remainder of the season but is unlikely to be given the role fulltime.
There is a handful of coaches available with A-League experience, including John Kosmina, Ian Ferguson and Miron Bleiberg, but there are unlikely to be a shortage of applicants from around the world.
Herbert has managed the Phoenix for more than 150 games since the club's inception in 2007, after being in charge of the New Zealand Knights for their His contract was due to expire at the end of the season before a two-year option on "football-related matters'' was meant to kick in.
It's not clear what the job of a technical advisor to the board would entail and whether it would mean he was a consultant or work with the academy.
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 it's unclear if the club are still pursuing this option.
"We certainly don't want to lose him,'' Morgan told RadioLive.
"Eventually, [director of football] is where it would be great to have Ricki because I don't think there's anybody in New Zealand football that's got as much knowledge and skill as that man.''
Chairman Rob Morrison later said Herbert's position would be reviewed at the end of the season.
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. A win over New Caledonia in Dunedin on March 22 will see the All Whites win the Oceania group.
Phoenix captain Andrew Durante and Greenacre are due to front media after training later this morning.