Manager John Hughes had recently been quoted as saying the 46-year-old was likely to pursue another opportunity.
Latapy confirmed his departure in a statement on the Caley Thistle website without revealing his destination.
"I have never hidden my ambition to one day be my own man in management terms and believe now is the time," he said.
"My journey here has been fantastic and I have enjoyed every minute of my time in Inverness, culminating in us finishing third in the SPFL and winning the William Hill Scottish Cup, a massive achievement for any club let all alone ICTFC."
Latapy, who thanked Hughes for giving him the opportunity to be his assistant 18 months ago after a spell in a similar role with Boavista in Portugal.
The former Trinidad and Tobago midfielder had been Hughes assistant at Falkirk before a spell as his country's national head coach.
Caley Thistle chairman Kenny Cameron said: "Whilst we are particularly sorry to see Russell depart for pastures new, we fully appreciate his desire to further develop his undoubted talents in a new environment.
"Russell will always be remembered here at ICTFC, as a member of a great winning team."
Cameron hinted that Caley Thistle were prepared for such an eventuality.
"I recognise that any form of organisational change brings with it its own range of challenges," he added.
"I am, however, confident in our abilities to mitigate these challenges and look forward to working with the board and the club management as we seek to secure future successes for ICTFC."
Russell Latapy has left his post as assistant manager with Inverness Caledonian Thistle saying it is time to become a boss in his own right again.