The City of Belfast Orange Widows Fund was allowed to sound only a single drum beat between Carrick Hill and Donegall Street - which includes St Patrick's church - during the parade on Sunday afternoon.
But as three bands marched the controversial part of the route, a hymn was played.
Around 20 nationalist protestors gathered at Clifton Street with a banner which read 'respect our community'.
There was a visible security presence in the area close to the church while the march took place.
In a further Parades Commission determination, no supporters were allowed to accompany the parade past the church.
The Donegall Street area has become a flashpoint since trouble broke out following a Black Institution parade at the end of August.
Meanwhile on the Twelfth of July members of a loyalist band were filmed marching in circles and playing a tune alleged to be sectarian outside the church.
Those taking part in Sunday's parade travelled to a church in east Belfast for a thanksgiving service, before leaving the Newtownards Road shortly before 5pm.
That parade made its way back along Donegall Street, where music was played again by bands. However, the march passed off peacefully, with a small protest by Carrick Hill residents.
Carál Ní Chuilín, Sinn Féin MLA for North Belfast, said: "This is fairly early on in what's become known as the marching season and I think the Loyal Orders in particular need to be very, very responsible in these areas.
"Everyone says they want a peaceful time, what they need to do is demonstrate how they're going to make that happen.
"The only way to make that happen is through dialogue, sitting down with residents and working out their issues," she added.
Father Michael Sheehan from St Patrick's Church said he was disappointed at the breach, but added that it was a dignified parade.