Mauger confirmed his departure in a statement on Monday, saying: "It's now time for me to return home to my family and give my best back to (my wife) Amy and my four beautiful children."
While Mauger stressed family reasons for his departure, Moana Pasifika's performance in its first two years has fallen below expectations.
The team, which combines players of Samoan, Tongan and Fijian heritage, won only two games in its debut season last year and has not managed a win this season with only two of 15 regular-season rounds remaining.
Mauger seemed to acknowledge in his statement his task as inaugural head coach had not been an easy one, noting "I have given everything for the cause in testing conditions."
"I love this team immensely and it has been an absolute privilege to be a part of this special journey for Moana Pasifika and broader movement for the Pasifika community," he said.
Moana Pasifika chairman Michael Jones acknowledged Mauger's contribution to the fledgling team.
There inevitably will be suggestions that Mauger was dealt an impossible hand.
After years of lobbying, Pacific nations finally achieved direct representation in Super Rugby when Moana Pasifika and the Fijian Drua were created.
But the Moana Pasifika team was left mostly with players left over the New Zealand Super Rugby franchises had had first choice.
All Blacks of Pasifika heritage remained with their New Zealand franchises and Mauger had to work with a group which had little international experience.
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