The press ad, headlined, "We are the champions", said: "Good luck in the Barclays Premier League, we're proud to sponsor you", following the team's final game of the season.
Waitrose signed a new two-year sponsorship with Reading in December 2010, which will include the team's 2012/13 season in the Premier League.
The high-profile sponsorship is also unique in that Reading is the only team to be sponsored by a supermarket chain.
The press campaign ran in The Sunday Times and also contained text stating, "Everyone at Waitrose would like to congratulate Brian McDermott [the manager] and his team at Reading Football Club on winning the npower Championship".
McDermott, the former manager of Woking FC and reserve team coach at Reading, has steered Reading to the Premier League after being entrusted with the full-time manager's job in January 2010, following a surprise victory against Liverpool in the FA Cup.
Follow Matthew Chapman at @mattchapmanUK