Sotheby’s followed up its Friday sale of books and manuscripts by auctioning three rare items associated with pivotal moments in American history.

A copy of the Emancipation Proclamation once owned by Robert F. Kennedy sold for $3.7 million, setting a record for presidential documents; an 1876 American flag used by General Custer during the Battle of Little Bighorn was bought by a private American collector for $2.2 million; and two typed pages written in 1891 by James Naismith setting the rules for a new game called “Basket...