Mr Johnson was killed by Monis during the struggle.
Barrister Katrina Dawson also died in the violent end to the siege as police stormed the Martin Place cafe in the early hours of December 16.
Macquarie St outside the church was partially closed during the service and dozens members of the public lined the street across from the church, having turned out for a final farewell.
Mr Johnson's father, Ken, read the eulogy at the service and wept as he spoke to Mr Scipione outside the church afterwards.
Mr Johnson's partner, Thomas Zinn, read a tribute and was first to exit the church after the service, which will be followed by a private cremation in Sydney's east.
Sydney Lord Mayor Clover Moore, federal Communications Minister Malcolm Turnbull and his wife Lucy and NSW Governor David Johnson were among the dignitaries at the funeral.
Lindt Australia chief executive Steve Loane attended and actor Steve Bisley was also among the mourners.
The huge floral tribute to Mr Johnson and Ms Dawson that has covered much of Martin Place was removed on Tuesday morning, ahead of expected rain.
The survivors were joined by Reverend Bill Crews, who led the service for Mr Johnson at St Stephens Uniting Church, just 100 metres from the Lindt Cafe.
They embraced in a group hug outside the marquee.
Bystanders continued to leave flowers after the survivors had left.
Mr Baird attended a service held in Martin Place with SES and Rural Fire Service volunteers as the work was completed.
A memorial service for Ms Dawson, a 38-year-old mother of three, will be held on Tuesday afternoon.
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- AAP