After a week-long trial at Ipswich Crown Court, Rev Canon Ian Finn, 58, was unanimously cleared of the charges against him by a jury.
Rev Finn had been accused of not handing over wedding and funeral fees to the Diocese of St Edmundsbury and Ipswich between 2007 and 2014 whilst he was the vicar at St Mary the Virgin Church in Haverhill, Suffolk.
Rev Finn blamed incompetence for the error in calculating the fees and had written out a cheque for £18,000 to cover the shortfall after he was summoned to an informal meeting to speak about the missing money in 2014.
After the verdict, Rev Finn tolk the East Anglican Daily Times he was "enormously relieved" to have his name cleared.
"The last three years have been a personal nightmare which I feared, during the darkest days, would never end. Despite today's verdict my life will never be the same," he said.
The Right Reverend Dr Mike Harrison, Bishop of Dunwich, said: "Many people in the Reverend Canon Ian Finn's parishes, as well as his colleagues and elsewhere, will be left deeply saddened by all that has happened.
"He has achieved a lot of good during his years of ministry, and is well thought of by many.
"Now the trial has concluded, the diocese will inevitably need to review the matter internally and decide what further action, if any, is required."