The former Stormont deputy first minister and ex-IRA commander died on Tuesday of a heart condition at the age of 66.
Among the mourners at St Columba's Long Tower Catholic Church were former US president Bill Clinton and Stormont first ministers Peter Robinson and Arlene Foster.
Bill Clinton received a round of applause from mourners
Alastair Campbell attended the funeral
A piper played as his coffin was carried onto the street and a tricolour flag as draped over the coffin by top members of Sinn Fein.
The funeral mass was lead by Fr Michael Canny.
In his homily, Fr Michael said that to see McGuinness' legacy, all you had to do was look around you.
"Look not at the beauty of this Saint Columba's Church, which was such an integral and important part of Martin's life.
"Look, instead, at the people gathered in this church, to say farewell to a man who was such a proud member of this community, the person who came to be a widely respected leader of this community, someone who has been acknowledged in recent days as a politician who spent year after year moving this community towards peace."
Arlene Foster and Bishop John McKeown arriving at the church
Fr Michael added that it would have been "unthinkable" for many of those in attendance to have been at McGuinness' funeral a generation ago.
"They have forged working relationships with Martin McGuinness; they have built friendships with him; they have occupied Stormont's benches alongside him.
"Some have even sat in government with him. You are all very, very welcome. The presence of those political rivals and opponents among you, who have come to pay their respects this afternoon, is the most eloquent testimony to the memory of Martin McGuinness."
Sinn Fein's Michelle O'Neill, Mary Lou McDonald and Gerry Adams during the funeral procession
The priest added that many people still struggle with McGuinness' past involvement in the IRA but told mourners to remember: "The word 'journey' has been used by many people in recent days to describe Martin's transition from man of war to man of peace. The word journey is also used frequently to describe the believer as he or she lives life on the way to union with God.
"In our Gospel we heard of the disciples' journey that began in darkness after the death of Jesus - having witnessed his crucifixion - but turned to hope when they discovered that he was not dead but alive.
"By any standards, Martin McGuinness was a remarkable man and his life was a remarkable journey. The values he had, the principles he championed are still very much alive."
Readings were read by McGuinness' nephew Odhran and his son-in-law Sean Hargan.
At the conclusion of the Requiem Mass, the remains of Martin McGuinness were taken to the City Cemetery for burial.