In an emotional ceremony at Liverpool Town Hall, Trevor Hicks, president of the Hillsborough Family Support Group, signed for the honour on the families' behalf.
"I do not think anywhere in the world could have been as supportive as this city has been," Hicks told those in attendance in the Grand Ballroom.
"It is with great honour and humility that I accept this."
Kenny Dalglish, Liverpool's manager at the time of Hillsborough, then lit a candle in memory of the 96.
The families were also joined at the ceremony by
Steven Gerrard,
Jamie Carragher, Rafa Benitez, Alan Hansen and Alan Kennedy.
Earlier in the day, a moving memorial service at Anfield was attended by an estimated 28,000 people.
Hundreds of floral tributes, scarves and a variety of different football shirts were laid next to the Hillsborough memorial and tied to the Shankly Gates.
The commemoration was opened by the Bishop of Liverpool, the Rt Rev James Jones, before the 96 names were read out and a candle lit in each of their memories.
At 3:06pm, a two-minute silence was impeccably observed at the stadium and across Liverpool as the city, including public transport, ground to a halt in memory of the 96. Similar silences were held in Sheffield and Nottingham.
The bells of Liverpool's two cathedrals and civic buildings then rang out 96 times at 3:08pm.
Liverpool Lord Mayor Cllr Steve Rotheram joined Hicks in giving a rousing speech before the Mayor and Liverpool manager Benitez symbolically laid a scarf on the penalty spot in front of the Kop.
The duo released 96 red balloons into the afternoon sky as Gerrard and Carragher presented Hicks with a Freedom of the City scroll to Hicks, on behalf of all the families.
The memorial concluded as Gerry Marsden sang an emotional rendition of You'll Never Walk Alone.
