The service has traditionally been held at Anfield but families of the victims decided 2016's ceremony would be the last at the stadium.
Instead, a "simple" service offered people "time for silent reflection", the Bishop of Liverpool said.
The Hillsborough families said the service was "scaled down a lot".
Ninety-six football fans were fatally injured in the crush at the FA Cup semi-final in Sheffield on 15 April 1989.
The new shorter service was the first held since inquests ruled their deaths were unlawfully killed.
Margaret Aspinall, whose son James died at Hillsborough, said it was "going to be different, a bit more personal and probably a bit more private for the families".
"We were all together before. Now I think it means that we can all reflect in our own way."
The half-hour service began at 14:45 BST, with one minute's silence held at 15:06 - the time the 1989 football match was halted as the disaster unfolded.
Future ceremonies will alternate between Liverpool's Anglican and Catholic cathedrals.
The Rt Rev Paul Bayes, Bishop of Liverpool, said it would be a "simple, prayerful service, offering the chance to continue to remember the victims of Hillsborough and pray for the families and all affected".
He added that it was "open to all who find it helpful to mark the anniversary in prayerful contemplation".
A memorial service to mark 28 years since the Hillsborough disaster has taken place at Liverpool's Anglican Cathedral.