The former One Direction singer's first solo single Pillowtalk has also topped the On Demand Songs and U.S. Digital Songs chart and reached number one in his native UK following its January 29 release.
Malik said: "Thank you to all my fans and supporters. We have achieved this together and I am grateful."
He also tweeted: "What is gwaning :) !! I can't explain the love and gratitude i feel today, thank you for making this happen (sic)."
Pillowtalk sold 267,000 downloads — the highest one-week sales of 2016 — and became the fastest song by a debut artist to reach number one on Spotify’s global chart.
It is also just the 25th song ever to debut on the top spot of the Hot 100.
This is Malik's first number one on the chart, he previously peaked at number two with One Direction's 2013 Best Song Ever.
Since Malik left the band in March 2015, they have reached number three with Drag Me Down and 10th place with Perfect.
Malik will release his debut album Mind of Mine on March 25, exactly one year after he quit the boy band.