Amityville-born and Massapequa-raised Baldwin started out his acceptance speech night by ribbing Donald Trump, saying the president finally has his Emmy.
The long-running sketch series also scored wins for Outstanding Variety Sketch Series and Outstanding Directing for a Variety Series, adding to the five awards it picked up at the Creative Arts Emmys last weekend.
Colbert devoted a significant portion of his opening comments to teasing Trump for having never won an Emmy, something Trump has often griped about.
Perhaps the most biting Trump commentary came, unexpectedly, from the crowd-pleasing reunion of Dolly Parton, Fonda and Tomlin, stars of the 1980 hit movie "9 to 5".
The actor won outstanding supporting actor in a comedy series for his role as the President on "Saturday Night Live".
Stephen Colbert, the 53-year-old Late Show host, who helmed the show, pointed out that Emmy voters made a big mistake when they did not give Trump an award for Celebrity Apprentice.
Other new faces included Donald Glover, the best comedy actor and also director for his hip-hop themed show "Atlanta".
Take, for example, Big Little Lies co-stars Nicole Kidman and Alexander Skarsgård.
"The Handmaid's Tale", author Margaret Atwood's dystopian tale of a society where women are forced into sexual servitude, led the early Emmys, winning for writer Bruce Miller, director Reed Morano and supporting actress Ann Dowd, who plays a brutal den mother.
The biggest political shocker was White House former Press Secretary Sean Spicer making a surprise appearance, and even he couldn't resist a dig at the administration.
But what Hollywood award ceremony would be complete without bashing Trump?
Baldwin was asked what he thought of Spicer's appearing on Sunday night's awards show.
"I have done jobs that you shouldn't respect or admire me for, too.so we have that in common", Baldwin said. "He and I have that in common I guess".