"Saturday Night Live" also had a big night with wins for Best Variety Sketch Series, Alec Baldwin as Donald Trump, Kate McKinnon as Hillary Clinton and Melissa McCarthy as Sean Spicer, who made a surprise appearance on stage to joke about the crowd size.
Show host Colbert, known for his left-leaning comedy, kept his wit on Trump during his monologue.
The Los Angeles ceremony on Sunday night saw victories for political satire Veep and Saturday Night Live (SNL) which has enjoyed a resurgence with its attacks on Mr Trump.
"If he had won an Emmy, I bet he wouldn't have run for president", Colbert told the A-list audience. Best supporting actress Ann Dowd gave a moving acceptance speech along with other stars such like Nicole Kidman and Elizabeth Moss.
Iran says United States seeking to undermine nuclear deal
In its efforts to undermine the deal, the White House has recently attempted to sway the IAEA's reporting on Iran. Yet even he says Iran is, at best, only in "technical" compliance with the accord.
"We did have a whole storyline about an impeachment, but we abandoned it because we were anxious that someone else might get to it first", she said. Donald Glover became the first African-American to win for comedy series directing.
Drama Series: "The Handmaid's Tale".
In the competition, several high-profile series failed to live up to expectations, including Westworld and Stranger Things, which both went home empty-handed.
He rolled out onto the stage on an electric version of the White House lectern, from where he used to take questions from members of the media.
"If I do get an Emmy tonight it should be for the most incomplete performance by an actor in a supporting role", Baldwin joked.
Supporting Actor, Limited Series or Movie: Alexander Skarsgard, "Big Little Lies".
- Video shows Kenneka Jenkins enter freezer alone
- Formula One: Hamilton wins crucial, chaotic Singapore GP
- Giro d'Italia announces 2018 race will start in Israel
- The Justice Department has reportedly opened an insider trading investigation at Equifax
- 'Pure speculation': British Home Sec dismisses Trump's Parsons Green tweets
- Sprint follows AT&T with free iPhone 8 offer for trade
- Criminal probe opens into 8 deaths at Florida nursing home after Irma
- Group recommends guidelines for teens getting tattoos
- Trump's Former Campaign Manager Was Reportedly Wiretapped By US Investigators
- Here's how Hurricane Jose could affect NYC