A motion which said they should be "welcomed and affirmed in the parish church" as part of the "long and often complex process" of transition was passed.
It also proposed that clergy are provided with guidance to help them offer services to mark the transition of a transgender person.
Rev Chris Newlands tabled the motion. He said: "I'm euphoric and exhausted. I think it was a good debate with some excellent contributions.
"I did think there were some comments which reflect some the extreme views which we would wish to counter. I'm getting so many messages from trans friends around the world."
Rev Newlands was referred to an amendment to his motion which proposed that the church determine the theological basis for any new liturgy or customs.
All three houses of the Synod - bishops, clergy and lay members - rejected the amendment proposed by Dr Nick Land of the Diocese of York.
Rev Newlands added: "Synod has changed - we have turned a corner. Since the February decision on sexuality, bishops have realised they cannot continue to do what they have always done."
He referenced a decision by clergy in February to a reject a bishops' report which said marriage should only be between a man and a woman.
The Archbishop of York, Dr John Sentamu, said during the debate: "The theology needs to be done but that can be done very quickly ... let's vote for it."
Rev Newlands' motion was voted 30 to two in favour by bishops, 127 to 28 in favour by clergy, and 127 for and 48 against by lay members.
The motion passed reads: "That this Synod, recognising the need for transgender people to be welcomed and affirmed in their parish church, call on the House of Bishops to consider whether some nationally commended liturgical materials might be prepared to mark a person's gender transition."