The crowd jeered so loudly at Mr Pence that the performance had to be paused multiple times, according to audience members.
Brandon Dixon – who plays Vice President Aaron Burr in the musical – delivered a message on behalf of the cast after the show.
“Vice President-elect Pence, we welcome you and truly thank you for joining us here,” he said.
“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.
“But we truly hope this show has inspired you to uphold our American values and to work on behalf of all of us. All of us.”
It was not immediately clear whether Mr Pence heard the speech in its entirety or made any response.
On Twitter, audience members pointed out the irony of a staunch conservative – who has spouted anti-LGBT rhetoric and championed anti-gay policies – attending a hip hop musical with a majority non-white cast, whose lead actor Javier Muñoz is openly gay and HIV positive and, has been at the forefront of the fight against stigma around HIV and Aids.
The impassioned plea to Mr Pence, offered by an African-American actor in front of a ethnically diverse cast, comes after Donald Trump vowed to deport three million undocumented immigrants immediately on taking office.
Some conservative commentators said the reaction to Mr Pence was disrespectful, and claimed it represented the reaction of the out-of-touch "elite", since tickets to the show reportedly cost hundreds of dollars.
Mr Trump's future second-in-command has struck an aggressive pro-life stance in the past and many Americans fear he will restrict access to family planning when he enters office.
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