The duo, who run the Baillie Gifford Japanese fund, continued to see off the challenge of First State's Jonathan Asante, who held the number one spot up until they toppled him in July.
Mr Asante, who manages funds including First State Latin America, First State Global Emerging Markets and First State Global Emerging Markets Leaders, retained second position when the latest investment performance figures for the three years to October 30 were compiled by financial publisher Citywire.
The joint ranking of Ms Whitley and Mr Brett, among asset managers in about 35 countries monitored by Citywire, slipped from 15th to 35th.
Mr Asante's ranking dropped from 57th to 98th.
Ms Whitley read experimental psychology at Oxford University.
She joined Baillie Gifford after graduation in 1980 and became a partner in 1986.
She has run the Japanese equities investment team since 2001.
Mr Brett joined Baillie Gifford's graduate scheme in 2003 after earning a PhD in psychology at Bristol University.
He had previously graduated from Cambridge University. He has worked on the Japanese fund since 2008.
The £412.36 million Japanese fund is weighted towards manufacturing, which constitutes 17.3% of its assets.
However, the fund's biggest holding is in telecoms company Hikari Tsushin.
Lesley Duncan, manager of the Standard Life Investments UK ethical fund, took fourth spot after seeing her UK-wide ranking rise from 164th to 114th.
John MacDougall of Baillie Gifford, was in fifth place for his stewardship of the firm's Japanese smaller companies fund.
In total, some 95 fund managers working for investment houses with a significant presence in Scotland qualify for a Citywire rating, which denotes positive performance.
The list is dominated by Edinburgh-based Baillie Gifford, which now has 21 Citywire-rated managers.
This follows the inclusion of Stephen Paice, manager of its European fund, and fixed income specialists Steven Hay and Sally Greig.
However, Elaine Morrison, manager of the Baillie Gifford managed and developed Asia funds, dropped out of the rankings.
Standard Life has the second largest group of rated managers at 13, up from 12 with the addition of Matthew Williams, manager of the Edinburgh house's Japan fund.
Citywire's rankings are based on risk-adjusted performance.