Democratic rival, Hillary Clinton, accused the Republican of encouraging Russia to engage in cyber-attacks against the US.
She added: “That’s because he’d rather have a puppet as president of the United States.”
Trump responded: “You’re the puppet.”
Clinton continued: “It’s pretty clear that you won’t admit that Russia has engaged in cyber-attacks against the USA, that you encouraged espionage against our people, that you are willing to spout the Putin line, sign up for his wish list, break up NATO, do whatever he wants to.
“And you continue to get help from him because he has a very clear favourite in this race.”
Trump was later asked by moderator, Chris Wallace, if he condemned Russian interference in the election.
Trump said: “By Russia or anybody else.
“I don’t know Putin. I never met Putin. This is not my best friend.”
After the comment, a tweet from 2013 quickly surfaced and became the most retweeted of the entire debate.
Which prompted a wave of mockery.
Trump continued to attack Clinton saying: “She doesn’t like Putin because Putin has outsmarted her every step of the way.”
The Republican presidential hopeful has previously said Putin is a better leader than Barack Obama.
He also claimed the US presidential election is “rigged” against him and said he may refuse to accept the result if he loses on November 8.
“I will tell you at the time, I will keep you in suspense,” he said when asked if he would accept the outcome of the vote.
Clinton branded the comment “horrifying” and said she was “appalled” Trump would try to discredit the election process and reject the democratic decision of the American people.