Gibbes will return to his home country of New Zealand after admitting he needed to return home following 10 years away.
The news comes just weeks after he was left in charge of coaching at the province following Les Kiss' exit as director of rugby.
Gibbes said: "Being a long way from home for the last 10 years has made me prioritize things above my career, and so I'll be returning at the end of this season for family reasons.
"The challenge ahead for Ulster demands the full attention of everyone involved - the management group, the team, the coaches and support staff. It is exciting and achievable.
"However, I cannot in good conscience provide my full attention for the journey ahead. My family and I have thoroughly enjoyed our time in Ulster and we're very grateful for the welcome and good spirit afforded to us.
"I wish the team and the club all the very best for the future, and I am grateful for their understanding and support."
Ulster's operations director Bryn Cunningham has said there is an ongoing review behind the scenes to work out the best way forward.
He said: "We'd like to thank Jono for his dedication thus far and I know that he will be fully committed to us until the end of the season.
"A review of the coaching structure is ongoing and the desired outcome of this will be to provide us with a strong, well-balanced coaching team and some long-term stability."