Omaze and Stewart raised $2,235,520 for NYCA, from a total of 47,048 people, across 78 countries. The highest donation received was $35,000, while the average donation was $45.50.
Matt Pohlson, co-founder of Omaze, tweeted that he would "miss the man (Jon Stewart)" but was proud to have raised $2.2 million with him for the foundation.
Pohlson went on to praise the comedian on Instagram saying Stewart was "one of the great honors" for Omaze, commending him on his performance over the past 16 years as a talk show host.
"Over the last 16 years, no one has done more than Jon to engage people around the issues that truly impact our lives and it's fitting that he leveraged his final show to raise over $2 million for this incredible cause," Pohlson said in a statement emailed to CNBC.
The lucky winner to meet Stewart was named Sameer, who took his wife to the final taping; he donated $100 to the cause.
—By CNBC's Alexandra Gibbs, follow her on Twitter @AlexGibbsy.