RNZ reporting Ardern greeted Colbert at Auckland Airport this morning, as she promised to do when she appeared on his show.
This afternoon, he posted the selfie with Ardern on social media, joking "she appointed me President of New Zealand! ... I think."
Tourism NZ spokesperson Lauren Vosper said the airport welcome was filmed and would be part of the segments produced for the Late Show, which will air next month.
Vosper said Colbert was filming all over New Zealand but wouldn't confirm how long he was in the country for.
Ardern and Colbert were also spotted on the street chatting with New Zealand comedian Alice Snedden earlier today.
The photo was taken by political commentator and Spinoff editor Toby Manhire and posted on his Twitter account. It's thought the photo was taken near Auckland's Morningside.
Colbert had been scheduled to make a surprise trip in March, but the plans were shelved after the Christchurch mosque shootings, which left 51 people dead.
Shortly after the attack, Colbert expressed his condolences during a taping and urged people to visit.