It began at 15:00 BST on Friday and will end on Monday at at 23:59 BST.
The "show of solidarity against online abuse" hopes to encourage companies to take a stronger stance against racist and sexist abuse by users.
Rugby union, cricket and rugby league have also joined the protest.
The Premier League released a statement prior to the four-day silence, saying it would not stop challenging companies "until discriminatory online abuse is removed from our game and wider society".
"We know that a boycott alone will not eradicate this, which is why we will continue to take proactive steps to call for change," the statement continued.
A number players posted a statement shortly before the protest began, while football clubs changed their Twitter feed icons to a blacked-out version of their logo.
Leeds United midfielder Kalvin Phillips wrote: "Disappointed that we even have to be doing this. Social media should be a safe space for everyone.
"I really hope main platforms make it a priority to eradicate online abuse from their system. It's already a problem in society, let's do more to stop it online as well."
Anti-discrimination charity Kick It Out says the boycott "signifies our collective anger", with football being joined by other sports.