Sales of "Purple Rain" and "When Doves Cry" give the music icon the top two spots on the countdown, while "Little Red Corvette", "Let's Go Crazy", "1999", "Kiss", and "Raspberry Beret" also hit the top 10, setting a new record - one more hit than Jackson managed following his death in 2009, reported Billboard magazine.
But Prince's sales success wasn't quite enough to put him in the mainstream Hot 100 top three, as the chart compilers also take into account radio play, social media activity and popularity.
Drake's "One Dance" and Lukas Graham's "7 Years" round out the new top three.
Fourth-placed "Purple Rain" leads eight Prince tracks in the new Billboard Hot 100 and Hot R&B/Hip-Hop Songs charts.
The chart news comes a day after three of Prince's albums graced the Billboard 200 top five.