For example, EMI-owned Parlophone recently became the site's most popular UK channel of the year, with 240 million hits, despite the ban.
However, YouTube said the "tens of thousands" of videos which had disappeared "will come back over the next few days".
"The music videos are an extremely popular part of YouTube and this deal doesn't only cover the music videos but also music included in TV programmes like the X Factor and also for the inclusion of music in user videos as well," YouTube's Patrick Walker told the BBC.
The deal will also mean that new material will appear on YouTube as the site signs partnerships with other record labels and guest editors introduce their favourite videos.
Pete Waterman says songwriters should get paid properly by YouTube
In the UK, PRS for Music acts on behalf of member publishers as a collecting society for licensing fees relating to the use of music.
At the start of the row Mr Walker told the BBC that PRS was seeking a rise in fees "many, many factors" higher than the previous agreement.
He said the two were "so far apart" that YouTube had no choice but to remove content while negotiations continued.
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