Stephen Palmer, 68, who was a curate in Stubbington in Hampshire at the time, was found guilty in May following a trial at Portsmouth Crown Court.
The court heard Palmer indecently assaulted the girl multiple times at his house in 1975.
The Diocese of Portsmouth said it was "distressed" by the conviction.
The court heard Palmer would wait until his wife had left the house to take their two children to school, before he would start assaulting the 17-year-old girl.
Sentencing him to 39 months in prison, Judge Nigel Lickley QC said Palmer, now of Turriff, Aberdeenshire, had abused his position in the church.
"You've shown or expressed little remorse for the charges against you," he said.
Palmer will have to serve at least half of his sentence before he can be considered for release, the judge said.
During his career, Palmer also served in the Isle of Wight, the Falkland Islands and as a Royal Naval Reserve chaplain, as well as being appointed as a chaplain to the Queen.
A statement issued by the Diocese of Portsmouth said: "Our thoughts and prayers are with the victim, who has had to live with the consequences of these assaults for many years.
"Since the 1970s, safeguarding procedures and policies have been transformed in the Church of England, as well as in society generally. The safety of the children and young people in our care is paramount."
A former chaplain to the Queen has been jailed for more than three years for indecently assaulting a 17-year-old girl 40 years ago.