The doodle shows the musician singing, his left hand raised to make the letter "l" in the word Google.
Born on October 13, 1948, Khan was primarily a singer of qawwali, the devotional music of the Sufis.
The singer died of a cardiac arrest at the age of 49 on August 16, 1997.
Last week, another Pakistani singer Ghulam Ali cancelled his concert in Maharashtra after Shiv Sena threatened to disrupt it.
Google last month celebrated the birth centenary of renowned Indian artist Maqbool Fida Husain (aka M.F. Husain) who died in London on June 9, 2011 where he would spend his summers after a self-imposed exile since 2006 due to death threats back home and scores of lawsuits.
Using some of the painter's favourite colours, notably pastels in blue, red, yellow ochre and mud brown, Goodle doodle was an abstract geometrical illustration with circles and M.F. Husain's painted portrait holding a brush at the centre.
The search engine called M.F. Husain the Picasso of India.
"This was partly due to his modernist, slightly cubist paintings and to the sheer volume of work he produced. His middle name, 'Fida' can be translated as 'obsessed' or 'devoted' which could also describe his approach to making art." Google said.