The city will also stage a vigil to show support for the victims' families following the disclosure of the Hillsborough documents.
The city's executive mayor, Joe Anderson, said: "With the release of these documents, we are hoping to get the truth of what happened more than 23 years ago.
"The importance of this day cannot be underestimated, as it will trigger the start of a process which will lead to justice for everyone affected by the tragedy."
The two-minute silence will take place at 3.06pm - the time the FA Cup semi-final was abandoned - as the bells at Liverpool Town Hall and other civic buildings ring out 96 times.
Flags at council properties will be flown at half mast throughout the day.
Tonight's vigil, taking place at Liverpool's St George's Hall from 6pm, will see the names of the 96 read out and a candle lit in memory of each one.
Relatives of the dead will be joined by representatives of Liverpool Football Club and community and religious leaders.
Mr Anderson said: "We know the city will want to stand shoulder to shoulder with those affected by Hillsborough and share their sadness together as a city and support each other through this emotional time."
The event is expected to finish at around 7pm.
Motorists are advised that some roads around St George's Hall will be closed and traffic diversions put in place.