The co-anchor of the NBC morning programme confirmed her departure plans during a live broadcast in May, saying that she wanted to spend more time with her family.
Matt Lauer opened this morning's show by saying: "Welcome to Today on a very bittersweet Wednesday morning."
Vieira, who was joined in the studio by her husband and dog, added: "It's tough, it's a hard one. Very mixed emotions. I'm looking at everybody right here... I know it's right but it's hard."
Her final Today broadcast included a surprise appearance by Carole King, who sang 'You've Got A Friend'. Lauer told viewers that the song "sums up the way we feel about [Vieira]" and shared that she once told him she listened to it 30 times in a row after graduating.
King said: "We are really going to miss you. It's been so amazing having you in our lives on a daily basis. Thank you so much for the memories."
Other farewell surprises include a video of Vieira's most memorable moments and a Today show group performance of 'Don't Stop Believing' by Journey, where Lauer led Vieira through the building as colleagues sang to her.
A huge crowd also gathered outside the plaza to say farewell to Vieira, who thanked them for coming out. "All of you I'm putting in my heart so I'll never lose you," she said. "I love you all very much."
Vieira's final show closed with Lauer, Al Roker, Natalie Morales and Ann Curry paying tribute to her work on the show and how much she has "changed" their lives.
"You have touched everyone and shown us from day one that this was all about you being just the way you are," said Morales, while Roker said he had never worked with anyone so dedicated to the programme or her co-workers.
Lauer admitted that he found it difficult to talk about Vieira's departure in public without turning to jokes and sarcasm because he was worried he would "become a blubbering idiot", but told her that he "adored" her.
"I have marveled over the fact someone who has a talent as large as yours, how small your ego is," he said. "You have taught us all how to be great teammates and that's the gift I'll take away from you."
"I don't want to go now!" joked Vieira. "I think life is about changing. One door closes and another opens. I love you all. You are the best. It's such a family and it's really hard to leave a family. I'm not going to say goodbye."
Vieira will be replaced as co-anchor by colleague Curry, while Morales will take over regular news reading duties and NBC News White House Correspondent and MSNBC anchor Savannah Guthrie will co-host the third hour.
> Meredith Vieira left 'Today' to enjoy life