The sportswear brand unveiled the 75 metre long billboard in London on 31 May, the day before Walcott was omitted from the 23-man squad and four days before Ferdinand was ruled out through injury.
The ad sees Ferdinand, Walcott and England players Wayne Rooney and James Milner replacing the original US Presidents in the Mount Rushmore sculpture.
A spokeswoman for Nike says Ferdinand and Walcott will not be replaced and the ad will run until 20 June as planned.
She adds Nike will continue to support Walcott, who “has the potential to make a big impact for his country in years to come”, while it “looks forward” to Ferdinand recovering to play again soon.
The move comes a week after Marks & Spencer said it stood by a campaign for one of its menswear ranges that features Walcott.
Nike will be hoping that no more of its football ambassadors are ruled out of the tournament, which starts on Friday (11 June).
The sportswear brand, which also has deals with Cristiano Ronaldo, Cesc Fabregas and Fernando Torres, is battling with Adidas to dominate the football market.
It is also kit maker to the USA and Brazil, and owns Umbro, which makes the England kit.