Where Are We Now? placing, at six, followed initial concerns by the Official Charts Company that its sales could not be tabulated.
David Bowie left his fans surprised and delighted when he released the track on Tuesday, his 66th birthday.
It was originally feared that sales of the song as a single track could not be differentiated from copies given free to those who pre-order his new album.
The track went straight to the top of the UK iTunes chart after it was put on sale.
Scream and Shout, will.i.am’s collaboration with Britney Spears, climbs one place from two to claim this week’s top spot.
The song becomes Britney Spears’ sixth UK number one single and her first since her solo effort Everytime topped the chart in 2004.
Taylor Swift’s track I Knew You Were Trouble moves up three places to two, while last week’s chart-topper James Arthur falls to third place with Impossible.
In the album chart, Emeli Sande’s Our Version of Events returns to the top spot at the expense of Calvin Harris’s 18 Months.
That record, number one last week, now sits at two, one place ahead of the self-titled debut album from songwriter Jake Bugg.
Rihanna’s Unapologetic drops to four, while the soundtrack for the new film of Les Miserables enters the chart at five.
David Bowie’s last Top 10 hit in the UK came 20 years ago when Jump They Say, from his 1993 album Black Tie White Noise, peaked at nine.
His most recent solo number one came 10 years earlier when the title track to his 1983 Let’s Dance record spent three weeks in pole position.
According to the Official Charts Company, Where Are We Now? sold 30,000 copies compared to Scream and Shout’s 62,000.
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