Network president Phil Griffin said on Thursday that "sometimes you just get one wrong - and that's what happened here."
Seder had been told last week that he wouldn't be welcomed back on the network after conservative commentator Mike Cernovich pointed out the apparent joke by Seder about defenders of film director Roman Polanski, a fugitive since pleading guilty to having unlawful sex with a minor in the 1970s.
In his tweet, Seder wrote that he didn't care about Polanski, "but I hope if my daughter is ever raped, it is by a truly talented man with a great sense of mise en scene."
Seder, a comedian who does the political podcast "The Majority Report," is an occasional presence on MSNBC, most often on Chris Hayes' prime-time show.
MSNBC's action provoked an online outcry from fans who thought the network was caving to pressure from conservatives.
"We made our initial decision for the right reasons - because we don't consider rape to be a funny topic to be joked about," Griffin said. "But we've heard the feedback, and we understand the point Sam was trying to make in that tweet was actually in line with our values, even though the language was not. Sam will be welcome on our air going forward."
MSNBC had initially said it wouldn't be renewing Seder's contract, which expires early next year.
Seder said he appreciated the network's reconsideration and "willingness to understand the cynical motives of those who intentionally misrepresented my tweet for their own toxic, political purposes.
"We are experiencing an important and long overdue moment of empowerment for the victims of sexual assault and of reckoning for their perpetrators," he said. "I'm proud that MSNBC and its staff have set a clear example of the need to get it right."
Cernovich, in a video posted online, called MSNBC's reversal "a great day for us." He said conservatives will be able to cite Seder's tweet in the future whenever they are criticized for tweets that others find objectionable.
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