The long-time presenter of the BBC's flagship football show has recently been embroiled in a political row after openly criticising the government's new asylum policy.
The BBC said it considered Lineker's "recent social media activity to be a breach of our guidelines."
The broadcaster also said it had been in "extensive discussions with Gary and team in recent days" and "has decided that he will step back from presenting Match of the Day until we've got an agreed and clear position on his use of social media."
"When it comes to leading our football and sports coverage, Gary is second to none.
"We have never said that Gary should be an opinion free zone, or that he can't have a view on issues that matter to him, but we have said that he should keep well away from taking sides on party political issues or political controversies."
Posting on his personal Twitter account on Tuesday, Lineker criticised Home Secretary Suella Braverman after she had announced new government plans to ban people arriving in the UK illegally from claiming asylum.
The plan has been put in place in an attempt to curtail a steadily rising number of people crossing the English Channel in small and unsafe boats.
In response, Lineker compared the decision and language used to "that of Germany in the 30s" - alluding to the rise of Naziism during that time - and sparking a wider debate on political impartiality within the BBC.
His comments have attracted widespread support on social media, with one tweet getting 235,000 likes, but have also drawn their fair share of critics.
Ms Braverman later hit out at Lineker's tweet when speaking on the BBC's Political Thinking podcast, saying it "diminishes the unspeakable tragedy" of the Holocaust.
Lineker has been the host Match of the Day since 1999 and is the BBC's highest-paid on-screen star, earning a reported £1.3 million last year.
The broadcaster recently came under criticism for a perceived "over-politicising" of their coverage of the World Cup in Qatar, with several leading pundits - including Lineker - openly criticising the decision to host the tournament in a region of the Middle East with such a questionable human rights record.
Former Arsenal striker and Lineker's colleague at BBC, often appearing with the former Leicester forward on the screen has shown his support by not featuring in Saturday's Match of the Day edition.
Later on, Match of the Day's other regular pundit Alan Shearer also tweeted to say he would not be appearing on the flagship programme on Saturday.
The BBC released a statement shortly after to say that Saturday's recording of the show would go on without a presenter or pundits, focusing instead on the Premier League games after a number of colleagues, including Alex Scott and Mark Chapman, expressed views distancing themselves from being on the broadcast.
Since then, major commentators of the network have also decided to remove themselves from the show.
