Khan's contract expired on January 31 and Snapdeal has not renewed it, sources said.
When contacted, a Snapdeal spokesperson said: "We would not like to comment on this."
The actor was also not available for comments.
Three months ago, the Bollywood superstar had made controversial comments on perceived intolerance in the country that evoked criticism from many quarters.
At an event, Khan had said his wife Kiran Rao had asked if they should move out of the country, as she feared for the safety of their child in a climate of insecurity.
Snapdeal had distanced itself from the remark, saying the comments made by the actor were "in his personal capacity" and it was in no way connected with them.
In January, Khan ceased to be the ambassador for the government's 'Incredible India' tourism campaign. Actors Amitabh Bachchan and Priyanka Chopra replaced Khan as the brand ambassadors for the campaign.
Currently, Snapdeal is not looking at replacing Khan with another celebrity, the sources said.
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