Souza's painting "Man and Woman Grinding their Teeth" executed in 1957 Souza borrows from traditional African art and cubism with both figures painted with mask-like faces and elongated features.
A catalogue brought out by the auction house shows Souza with the work in his studio in a photograph taken by Ida Kar in the same year it was painted.
The large-scale work was formerly owned by Harold Kovner, a wealthy American hospital owner and collector who was a great supporter of the artist during a critical period, auctioneers said in a statement.
"Since then he has been a patron collector and gallerist instrumental in making Amsterdam the unlikely artistic and creative haven for many Indian contemporary artists," according to the auctioneers.
"This is the second of the year 2014's four sales for international department that is set to conclude with our second sale in India, to be held in Mumbai this December," the auctioneers said.