Canon Giles Goddard has been officially welcomed as priest-in-charge of St John's Waterloo with St Andrew's Short Street.
The new parish priest succeeds Canon Richard Truss who retired last autumn.
The licensing took place at St John's on Tuesday to coincide with St Giles Day.
"The global and the local can all be seen in the life of this parish," said the Bishop of Kingston Richard Cheetham during his sermon.
"These churches will I hope be communities of prayer, wisdom and salvation."
Turning to divisions in the wider church, the bishop added: "I hope and pray that this will be a place of 'relational theology' where people discuss their deepest beliefs."
He described Giles Goddard as being committed to local people and "someone who cares about the future shape of our tradition".
"I am looking forward to becoming engaged in different parts of this parish," responded Canon Goddard who indicated that the next few months in Waterloo would be ones of discovery for him.
Simon Hughes MP and Coin Street Community Builders director Iain Tuckett were among those who formally welcomed the new priest to Waterloo during the service.
Music was provided by a string quartet from the Southbank Sinfonia which is based at St John's.
Deputy Mayor of Lambeth Irene Kimm was joined by Deputy Mayor of Southwark Robin Crookshank Hilton as a small section of parish along with St Andrew's Church fall within the Borough of Southwark.
Tim Scott, rector of the adjoining Christ Church Southwark parish, was present to hear the Bishop announce plans for a closer partnership between all three churches over the next five years "in this dynamic part of London".
Clergy guests from outside the area included Canon Giles Fraser of St Paul's Cathedral and George Bush, rector of St Mary-le-Bow.