The president-elect later complained that the cast had been rude to Pence and harassed him during the late yesterday performance. "This should not happen!" Trump tweeted.
The wildly popular hit musical, which won 11 Tony Awards in June, follows young colonial rebels who became America's founding fathers, celebrating diversity and immigrants' contribution to the nation.
The show's lead actor, Javier Munoz, is openly gay, HIV positive and a cancer survivor.
Brandon Victor Dixon, who plays former vice president Aaron Burr, read a statement to Pence during the curtain call that echoed some of the main concerns critics have voiced since the Republican firebrand won the election on November 8.
With that, a performance about a revolution and dawn of a young nation became even more political.
Pence is a stalwart Christian conservative from the Midwest.
Thanking him for attending the performance, Dixon asked him to "hear us out."
"We, sir, we are the diverse America who are alarmed and anxious that your new administration will not protect us, our planet, our children, our parents or defend us and uphold our inalienable rights, sir," Dixon said.
Hamilton, Dixon told Pence, was performed by "a diverse group of men, women of different colors, creeds and orientations."
The audience cheered and loudly applauded.
The crowd had greeted Pence with a mix of boos and cheers when he entered the theater before the show.
During the performance, the audience gave a standing ovation at the line "immigrants we get the job done," theatergoer Christy Colburn tweeted.
"Crowd went NUTS at King George's lines 'when people say they hate you' & 'do you know how hard it is to lead?' He had to stop the song."
Trump complained in a tweet Saturday morning.
"Our wonderful future V.P. Mike Pence was harassed last night at the theater by the cast of Hamilton, cameras blazing," he wrote. "This should not happen!"
"The Theater must always be a safe and special place," he added in another message. "The cast of Hamilton was very rude last night to a very good man, Mike Pence. Apologize!"
Trump has deployed polarizing rhetoric to describe immigrants, vowing to build a wall along the US border with Mexico and ban Muslims from entering the United States.
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