The Manchester United manager confirmed that his father had passed away on Sunday evening at the age of 79 after suffering with ill health for several months.
Mourinho, who helped carry the coffin into the church, was joined by wife Matilde, daughter Matilde, son Jose Jnr and United assistant coach Silvino Louro for the service.
United goalkeeping coach Emilio Alvarez Blanco and Mourinho's assistant at Real Madrid, Aitor Karanka, were also on hand to support their friend.
A large crowd gathered outside the venue as Mourinho helped remove the coffin from the hearse before draping a large flag over it.
As a footballer, Mourinho Felix played first for Vitoria Setubal and then for Belenenses, making 274 appearances in the Portuguese league between 1955 and 1974.
He achieved one international cap for Portugal, appearing as a late substitute in a match against the Republic of Ireland in the 1972 Brazil Independence Cup.
After hanging up his gloves, Mourinho Felix became a coach with a number of Portuguese clubs including Uniao Leiria, Amora, Rio Ave, Belenenses and Vitoria.
Belenenses confirmed the news of his death in a statement which read: 'Os Belenenses CF have been made aware of the passing of Jose Manuel Mourinho Felix, club goalkeeper from 1968 until 1974, team coach in the 1970-71 and 1982-83 campaigns, and a much loved figure at the club.
'During this difficult time, the Belenense family and Os Belenenses CF sends its warmest condolences to his family, especially his wife and son, Jose Mourinho.'
Mourinho, who visited his ailing father regularly over the past few months, took to Instagram on Monday to share a touching black-and-white image of himself as a young boy with his father following his passing.
The country's football federation sent 'the most heartfelt condolences to Mourinho and the rest of the bereaved family.' United also extended their condolences on their official website.
The former Chelsea boss was pictured in Setubal on Monday evening after returning to his native Portugal ahead of Tuesday's burial.
Mourinho was seen being comforted by a friend as family and those close to Felix gathered ahead of Tuesday's church service.
The 54-year-old is due to return to Carrington for pre-season training on July 8 as United begin their preparations for the new Premier League season.
Mourinho and his players will travel to America for five high-profile friendlies against LA Galaxy, Real Salt Lake, Manchester City, Real Madrid and Barcelona.
They also take on Norwegian outfit Valerenga in Oslo and Sampdoria in Dublin before facing Champions League winners Real Madrid for a second time in the UEFA Super Cup in Skopje, Macedonia on August 8.