The Premier League match is the first between the two fierce rivals since the publication last week of an independent report into the Hillsborough stadium disaster which exonerated Liverpool fans of any blame in the 1989 tragedy that claimed 96 lives.
Sunday's occasion is likely to be highly emotional with players and staff having urged fans all week to show each other respect.
In Ferguson's letter, which will be handed to away fans entering Anfield, he says United "stands with our great neighbours Liverpool".
"Our rivalry with Liverpool is based on a determination to come out on top - a wish to see us crowned the best against a team that held that honour for so long," he adds.
"It cannot and should never be based on personal hatred. Just 10 days ago we heard the terrible, damning truth about the deaths of 96 fans who went to watch their team try and reach the FA Cup final and never came back," said Ferguson.
"What happened to them should wake the conscience of everyone connected with the game."
An anti-Liverpool chant of 'it's never your fault, always the victims' was heard from some quarters at Old Trafford last weekend in United's 4-0 victory over Wigan Athletic.
Some United fans said those chants did not refer to Hillsborough but to the fallout from the Luis Suarez-Patrice Evra race row last season.
Liverpool forward Suarez was banned for eight matches for racially abusing United defender Evra at Anfield in October.
FLORAL TRIBUTES
Former Liverpool striker Robbie Fowler suggested Evra and Suarez should lay floral tributes before Sunday's game to mark the tragedies both clubs have suffered.
Fowler told BBC radio it would be appropriate for the pair to help defuse the tension by showing unity before kick-off.
"It would be nice for Luis Suarez to put some flowers at the United end regarding the 1958 Munich air crash and for Patrice Evra to do so at the Kop," Fowler said.
"The two clubs do have a rivalry but some things are far more important than football and this is one of them."
Eight United players and three club staff were among 23 people killed in Munich.
Suarez refused to shake Evra's hand before the start of the last game between the two clubs at Old Trafford in February.
Tributes have been paid to the 96 who died at Premier League matches since the Hillsborough report was issued, with Liverpool's neighbours Everton staging a particularly poignant one before the match with Newcastle United at Goodison Park on Monday.
United defender Nemanja Vidic, who has been sent off twice at Anfield, believes the Goodison spirit should be taken into Sunday's game.
"We have to show an example and be on top of the situation and behave well.
"There is a lot of history with these two clubs. We have had some tragedies, they have as well. I think we should respect each other because we are big clubs and clubs that are respected in the world."
Two United fan groups, the Manchester United Supporters Trust and the Stretford End Flags, have urged supporters not to sing disparaging songs about the Hillsborough disaster.
Rival fans have sung distasteful chants about Munich in the past.
Liverpool go into the match fourth from bottom and without a league win this term although they beat Swiss side Young Boys 5-3 in Berne in the Europa League on Thursday.
United have won three of their four league games, are second in the table and beat Galatasaray 1-0 in the Champions League on Wednesday.
