But Trump called him to the stage after saying, "they're very special, they've done an incredible job for us". But Fox News addressed the incident on Election Day, calling it "an unfortunate distraction".
Pollsters, who largely failed to predict Mr Trump's victory over Hillary Clinton two years ago, were more reluctant to commit themselves ahead of these midterms in which the presidency is not up for grabs but the shape of federal and state government is.
As observers pointed out, Fox News journalists were among the "people in the back" that Hannity insulted. We have an extraordinary team of journalists helming our coverage tonight, and we are extremely proud of their work.
Already No. 1 in the cable news ratings, Fox has had a strong fall with the campaign and hearings for Supreme Court Justice Brett Kavanaugh, with Hannity leading the way.
The Trump campaign, however, had touted that Hannity and Rush Limbaugh would be "special guests" in a press release hours before the event.
A spokeswoman for the parent company referred an inquiry to Fox News, which did not elaborate on whether Hannity had been reprimanded in any other fashion.
Hannity's appearance meant either Fox lied Monday about its collaboration with the Trump campaign, or that it has no control over Hannity, said Angelo Carusone, president of the liberal think tank Media Matters for America, which has unsuccessfully called for an advertiser boycott of Hannity's show in the past.
And Hannity wasn't the only Fox host to take the stage to fawn over the president.
Hannity tweeted late Tuesday that the election results had been "a massive win" for Trump and the Republicans whom the president had campaigned for.
Trump was expected to address the results in greater detail at a White House news conference later Wednesday.
Their speeches weren't televised on Fox News, but were seen on C-SPAN.
One Fox News employee described to CNN Business the scene at the NY headquarters of Fox News at the time, as a number of journalists inside the company's news division watched the episode unfold live. He referred to the other reporters as "fake news".
Sean Hannity's has stated repeatedly that he is not a journalist.
"What I said in my tweet yesterday was 100% truthful". Hannity posted, "When the POTUS invited me on stage to give a few remarks last night, I was surprised, yet honored by the president's request".
Here's what's happening. Let me read a couple quotes of what some of these Fox News staffers have had to say. "They do awesome work day in and day out in a fair and balanced way and it is an honor to work with such great professionals", he posted. "Anyone doing business with Fox News should worry about the network's inability to enforce even the most bare minimum standards".
Hannity's role at the rally had been put in question by Trump campaign itself.
While Hannity has been able to get away with breaking normal protocol, the network had previously attempted to rein him in.
Hannity was rebuked by Fox in 2010 when the Tea Party advertised he would be appearing at one of its rallies. "This was NOT planned", he said.