Fraser, a former world number one and winner of 19 Grand Slam titles during the amateur era, died aged 91 earlier this month.
Australian former tennis players Lleyton Hewitt, Todd Woodbridge and John Fitzgerald were among the mourners at a service at Melbourne's St Patrick's Cathedral.
Fitzgerald read out a letter from Swiss legend Federer to Fraser's widow Thea, local media reported.
"I'm deeply saddened to hear of Neale's passing... he was a true legend," Federer wrote.
"I always enjoyed his company when we met around the world."
Fraser won three major singles titles, including a memorable Wimbledon final in 1960 when he beat Rod Laver, and 16 Grand Slam doubles crowns.
Speaking soon after his death, Laver called him "my dear mate" and "a true gem in a golden era of Australian tennis legends".
In 1959 Fraser won all three US titles -- singles, doubles and mixed -– at Forest Hills and led Australia to glory in the Davis Cup, a competition he became synonymous with.
He captained the team for 24 years, steering them to four tournament wins, often saying: "I could never think of anything better than representing your country."
