Match of the Day: 'Great to be here', says Lineker as he makes TV return
Pundit Alan Shearer said it had been a "really difficult situation for everyone concerned" as he welcomed Lineker back.
"It's good to get back to some sort of normality," he added.
Lineker was taken off air following a critical tweet on the government's asylum policy.
Last Saturday's Match of the Day was broadcast without presenters or commentary and was only 20 minutes long after many of Lineker's BBC Sport colleagues, including Shearer, walked out in "solidarity".
On Monday the BBC said it would launch an independent review of its social media guidelines, particularly for freelancers like Lineker, 62 - but he could return in the meantime.
At the start of the BBC's live coverage of Manchester City v Burnley in the FA Cup on Saturday evening, Shearer said: "I just need to clear up and wanted to say how upset we were that all the audiences who missed out on last weekend.
"It was really difficult situation for everyone concerned, and through no fault of their own some really great people in TV and in radio were put in an impossible situation.
"That wasn't fair. So it's good to get back to some sort of normality and be talking about football again."
Lineker added: "Absolutely echo those sentiments."
Earlier, he tweeted a picture of himself on set at the Etihad Stadium and wrote: "Ah the joys of being allowed to stick to football."
The BBC confirmed it had asked Lineker to step back from his TV duties in a statement last week, after Lineker described the asylum policy as "immeasurably cruel policy directed at the most vulnerable people in language that is not dissimilar to that used by Germany in the 30s".
His agent Jon Holmes wrote that the former England striker thought he had permission to voice an opinion on such matters.
"Gary takes a passionate interest in refugees and immigration and, as he saw it, had a special agreement with Tim Davie, the BBC's director general, to tweet about these issues," Jon Holmes wrote in the New Statesman.
Mr Davie has said he is committed to looking at how the corporation's impartiality guidelines apply to freelance staff, acknowledging there are "grey areas".
He apologised for what he acknowledged had been "a difficult period" for staff, presenters and audiences - and described the BBC's commitment to freedom of expression and impartiality as a "difficult balancing act".
He also denied his deal to get the presenter back on air was a "climbdown", telling BBC News: "I've always said we needed to take proportionate action."
After the official BBC statement statement was published, Lineker tweeted: "I have been presenting sport on the BBC for almost three decades and am immeasurably proud to work with the best and fairest broadcaster in the world. I cannot wait to get back in the MOTD chair on Saturday."