The flyover went from Sumner to Cathedral Square, over Hagley Park, and back to Christchurch Airport.
SOFIA will then leave the city for good about noon on Thursday when the crew make their way home to California via Hawaii.
For 10 years the aircraft has helped scientists collect data that would be missed by a telescope on the ground - but it was being shut down as new technology supersedes it.
NASA project scientist for the SOFIA mission Naseem Rangwala said Ōtautahi had become a home away from home for the California-based aircraft.
"Christchurch has played a big role in SOFIA's scientific success, and that will remain forever. Our team has formed very deep friendships and relationships with the people of Christchurch," she said.
This was SOFIA's seventh trip here, where it would spend 32 nights off the ground. The plane takes 10-hour trips at a time, flying above 39,000 feet to surpass 99 per cent of the Earth's infrared-blocking atmosphere.
Its recent final mission had a special focus on mapping magnetic fields in the Milky Way, alongside a range of other celestial phenomena - something that's made possible by the local climate.
"The reason we come to New Zealand is also because the air is much dryer, so our scientists, our astronomers love flying out of New Zealand."
Rose Swears, a Rocket Lab scientist and previous NASA intern, is one of the lucky few who joined the last mission.
"I'm so excited that I'm on board, and I'm so excited that I get to fly along, because everyone wants to do this," she said.
She said SOFIA was a unique piece of technology.
"Normally the atmosphere is in the way, and the pollution is in the way, but SOFIA gets above that. It's amazing that we can fly out of Christchurch and see things that are so far out in space."
Another one of the final few who visited the aircraft recently was Sophie Ineson, a 14-year-old space fanatic from Dunedin.
"Being here is just so overwhelming," she said.
"It's just so amazing to see all the stuff that goes on behind the scenes."
She was spotted by the US Embassy after advocating for more girls to be educated about career pathways into space.
"I wrote to the prime minister saying that we need more Kiwi mentors, women mentors for younger kids, for space and science in general."
She said the trip see the SOFIA ignited her excitement about a career in science communication.
Rangwala said it would be a bittersweet final departure for staff who have completed hundreds of missions with SOFIA.
"We will be celebrating because of 10 years of very successful science operations on this unique, complex, amazing platform. We will be cheering together and holding hands, and we will be saying goodbye to SOFIA."
SOFIA will now head back to California where its final months of operation will take place until October 1.