Most Rev Dr John Sentamu declared the church as Hull Minister during an open-air service, to reflect its regional significance in the Church of England and contribution to local communities.
During his sermon at the landmark, Dr Sentamu said: "In this re-designation, God by his spirit is doing a new thing - offering to all who receive it a fresh start with God and with each other in this City of Culture 2017."
The Archbishop made a symbolic voyage to Hull along the Humber estuary, leading a flotilla of vessels from on board the trawler My Mate.
He carried a lantern containing a flame lit at Holy Trinity's mother church, All Saints in Hessle, East Yorkshire, to symbolise its 700 year old medieval origins.
Vicar of Hull Minster, the Rev Canon Dr Neal Barnes, said: "It has been an enormous privilege for me to be Vicar on such a historic day for the church and the city of Hull.
"It has been a great joy that we have been able to share the day with so many people from Hull and further afield.
"We are immensely grateful to the crowds of people who made the pilgrimage to Trinity Square and contributed to an unbelievable atmosphere."
The re-dedication of Holy Trinity as Hull Minster is one of several occasions during a year the East Yorkshire city has been declared the UK City of Culture.
Councillor Stephen Brady, Leader of Hull City Council, said: "This is an incredibly important day, not just for Neal Barnes and his team, but for the city of Hull.
"Holy Trinity has always been a huge draw for visitors, but its new status as Hull Minster will elevate this to a new level and to have the accolade awarded during our year as UK City of Culture is a real coup.
"I am really proud of the strong partnership between Hull City Council and Hull Minster and I am looking forward to seeing Trinity Square and the wider Old Town welcoming a whole host of new visitors as the area springs back to life."