He initially worked under Paul Sturrock, before replacing the Scot as Argyle boss in December 2009.
Mariner, who asked to be released from his contract on Thursday, had reverted to the number two role at Home Park under Peter Reid this season.
Mariner's departure comes with Plymouth facing the threat of being wound up next year, unless the club can pay off their £760,000 tax bill to HM Revenue and Customs.
The former England striker made 135 appearances for the Pilgrims between 1973 and 1976, scoring 56 goals.
Source: BBC Sport
Source: BBC Sport