The recording, taken from the 1939 film The Wizard of Oz, entered the charts at number two.
It was more than 5,000 sales short of this week’s chart-topper Need U (100%) by Duke Dumont featuring A*M*E.
The Official Charts Company described Ding Dong The Witch Is Dead as “one of the most controversial chart contenders of all time”.
Sales were fuelled by an online campaign organised by opponents of the former British prime minister, who wanted to see the 51-second song reach number one.
Some Tory MPs demanded the BBC ban the song – but others warned that politicians should not interfere in the choice of records played by broadcasters.
New BBC boss Tony Hall has explained the broadcaster’s decision to only play a five-second clip of the song as part of a news item during the Radio 1 chart show, saying: “I personally believe it is distasteful and inappropriate.
“However, I do believe it would be wrong to ban the song outright as free speech is an important principle and a ban would only give it more publicity.”
On Sunday evening the Radio 1 chart show played a short segment of the song for just a matter of seconds.
Music reporter Sinead Garvan explained the context of the single’s appearance in the charts to listeners of the station, which has a target audience of 15- to 29-year-olds.
“Tributes poured in from across the world for Margaret Thatcher when she died on Monday, but there were also people who threw street parties around the UK,” she said.
“An online campaign began in 2007 to try to get this song, Ding Dong The Witch Is Dead, to number one in the charts the week Lady Thatcher died.”
Punk song I’m In Love With Margaret Thatcher by the Notsensibles, which was featured in recent film The Iron Lady, also entered the top 40 on Sunday.
The 1979 single reached number 35 after a push from fans of Thatcher in response to Ding Dong The Witch is Dead and sold 8768 copies.