Judge Alison Sinclair said the money was "frittered away'' on a car and holidays, as well as wine and food in the restaurant Kirkpatrick owned.
She said the eventual cost to AUT and its insurer, which investigated the fraud, was more than $1 million.
"You have nothing to show for all the money you took from AUT and I'm reminded you also continued to draw a salary.''
When Kirkpatrick started at AUT, he was on an annual income of $90,000.
He was on $150,000 a year when, in July this year, he went to Thailand on a holiday and was found out.
Crown prosecutor Rachael Reed said a colleague of Kirkpatrick's discovered a bank statement lying on his desk.
Invoice templates were also found and Kirkpatrick resigned soon after.
Ms Reed said Kirkpatrick had spent the money on "some form of lavish lifestyle''.
"The Crown's submission is that this is a man who had no need to steal but he had tastes beyond his means.''
Kirkpatrick's lawyer Russell Fairbrother said his client had chosen to sell his house as soon as the theft was found out but could not pay back more than $20,000 from the proceeds of the sale.
"Mr Kirkpatrick would love to make good the harm he has done. He is simply not in a position to do that.''
Judge Sinclair described that figure as a "drop in the ocean'' compared to the amount of money lost by AUT and its insurer.
She said the offending amounted to a breach of trust.
"You were held in high regard and you abused the trust and the the employee relationship.''
Judge Sinclair said Kirkpatrick had undergone psychiatric counselling and appeared to have a "misaligned'' personality.
"Although you present as a confident individual, you are a person lacking in confidence and are an introvert. This is also seen as an element which led to your offending.''
She gave him a discount for his early guilty plea, remorse and his co-operation with police.
Kirkpatrick has a long history in the Anglican Church and until recently was the priest in charge of St Albans in Balmoral.
Before moving to Auckland, he was also the vicar of St Michael and All Angels in Christchurch.
Kirkpatrick has a high profile as a gay-rights advocate within the church and was formerly in an 18-year relationship with Tim Barnett, the former Christchurch Central Labour MP.
In August 1998, he broke his back when he was thrown from a car after Mr Barnett fell asleep at the wheel and ran off the road in Dunedin.
