Matthews' self-described "bad" analogy deepened the discontent that the presidential candidate and his supporters have been feeling lately toward the cable network, one that is usually friendly territory for liberals.
"Sen. Sanders, I'm sorry for comparing anything from that tragic era in which so many suffered, especially the Jewish people, to an electoral result in which you were the well-deserved winner," Matthews said at the opening of his show, "Hardball," on Monday evening.
He said he'd try to do a better job elevating the debate this campaign season. He made the Nazi remark during his network's coverage of Nevada results on Saturday night.
Even before Matthews' analogy, a report in The New York Post said the Vermont senator had confronted MSNBC's president, Phil Griffin, before the Las Vegas debate last week and said the network had not been fair to his campaign. MSNBC would not comment on the story.
In some respects, it recalls tweets of protest that come from President Donald Trump when he hears things he doesn't like on Fox News Channel, the network where many of his fans congregate. MSNBC has a liberal prime-time lineup led by Rachel Maddow, while conservatism reigns at Fox, led by Sean Hannity.
Matthews had said Saturday that he was reminded of a French general reporting to British Prime Minister Winston Churchill that France had fallen to Germany in the summer of 1940.
"Churchill says, 'how can it be over? You've got the greatest army in Europe. How can it be over,'" Matthews said. "He said, 'it's over.'"
Sanders' communications chief, Mike Casca, tweeted that he "never thought part of my job would be pleading with a national news network to stop likening the campaign of a Jewish presidential candidate whose family was wiped out by the Nazis to the third Reich. But here we are."
It wasn't even the only Nazi reference on the network last week. Chuck Todd had earlier read from a commentary in the digital publication The Bulwark that compared Sanders supporters to a "digital brownshirt brigade" that hounded opponents and enforced discipline — much like Trump's.
MSNBC's Nicolle Wallace also commented about how the Sanders campaign, like Trump's, had engaged in the "dark arts" of abusing and bullying the press.
"What do we miss in terms of paying attention to a squeaky, angry minority and ignoring the majority?" she said.
Casca did not immediately return calls seeking comment on other examples of what had set off the campaign. It was notable that at Sanders' victory party in San Antonio on Saturday night, the televisions were tuned to CNN, not MSNBC.
MSNBC contributor Anand Giridharadas commented on the network Sunday that MSNBC and the Democratic power structure are stuck in an old way of thinking and missing what may be going on.
"It is time for all of us to step up, rethink and understand the dawn of what may be a new era in American life," Giridharadas said.
An MSNBC spokesperson said that "we don't owe fawning coverage to a Democratic campaign. We owe fair coverage."
The network may be caught in a situation similar to news networks when Trump took over the Republican Party in 2016 — with a lineup of anchors and contributors light on supporters of the party front-runner and stocked with old hands. Matthews is a veteran commentator and newspaper columnist who was chief of staff to House Speaker Tip O'Neill in the early 1980s. Prime-time host Lawrence O'Donnell was an aide to the late Sen. Daniel Patrick Moynihan in the early 1990s. Wallace was a Republican who worked for President George W. Bush.
A study last fall by the liberal digital magazine In These Times criticized MSNBC for not covering Sanders as much, or as positively, as rivals former Vice President Joe Biden and Sen. Elizabeth Warren. But at the time, Biden was the presumptive front-runner and Warren was surging, so it's not surprising that conventional wisdom would reflect more positively on those two campaigns.
The Sanders team's discontent with MSNBC didn't prevent campaign manager, Faiz Shakir, from appearing on the network Monday for an interview with Stephanie Ruhle.
When asked by Ruhle about criticism from veteran Democratic strategist James Carville about the Sanders campaign, Shakir showed disdain for the old order.
"I'm not worried about James Carville," Shakir said. "He's a political hack."