Ferguson, 37, who plays uptight lawyer Mitchell Pritchett on the hit ABC sitcom, and Mikita, 27, a real-life lawyer, became engaged last year when the two vacationed in Mexico, after being together nearly two years.
Playwright and screenwriter Tony Kushner officiated the ceremony, according to Ferguson's rep.
"Never been happier. XO Goodnight!" Ferguson Tweeted early Sunday morning.
Among those in attendance: Nigel Lythgoe, Cat Deeley and Mary Murphy from Ferguson's So You Think You Can Dance guest-judging gig.
"I think the service at Justin and Jesse's wedding was so beautifully honest," Lythgoe Tweeted. "It was so emotional that when we weren't laughing we were crying."
The actor's Modern Family costar Julie Bowen later dubbed the N.Y.C. affair the "#bestweddingever."
Despite residing in California, the Montana-born Ferguson explained last month on The View – a day after the historic June 26 Supreme Court ruling that called the state's Prop 8 unconstitutional – that the couple had already made plans to marry in New York, because "that's where it was legal."
He added, "It wasn't legal in California up until yesterday. Weddings are expensive, y'all, and we wanted to give that money to a state that accepted us as an equal. We're too far down the planning path to change."
One thing on which the couple promised they'd spare no expense is good drinks for their guests.
"We really want a great mixologist for a craft cocktail bar," Mikita told PEOPLE earlier this year. "There are some great New York speakeasies, like Milk and Honey. So we're trying to bring a cool vibe like that to our wedding."
In lieu of wedding gifts, the couple asked that guests donate to the marriage equality charity Tie The Knot, to help other same-sex couples win equal rights in other states.
Husband.— Justin Mikita (@JustinMikita) July 21, 2013