Philadelphia's Joel Embiid won MVP with Jokic finishing second. Jokic, who won back-to-back MVP awards the previous two seasons, finished with 15 first-place votes, 52 second-place votes and 32 third-place votes for a total of 99 votes out of 100 ballots.
The NBA released the MVP voter selections on Thursday and Jackson's ballot had Embiid first, Milwaukee's Giannis Antetokounmpo second, Boston's Jayson Tatum third, Oklahoma City's Shai Gilgeous-Alexander fourth and Cleveland's Donovan Mitchell fifth.
"One thing I live by, you make a mistake, you own it," Jackson said in an interview with SiriusXM NBA Radio's Justin Termine and Eddie Johnson. "Absolute mistake made by me... In thinking how did I make that mistake: you can tell I put one center, two forwards and two guards. So I wasn't even thinking.
"I apologize to the Denver Nuggets. I apologize to Nikola Jokic, who is not only in the MVP discussion and deserved to be on my ballot but he is one of the greatest players in the history of this game and a top-10 center of all-time. So I own it. If you want to take away my vote or do whatever, more than welcome. I made a mistake."
Jokic nearly averaged a triple-double with 24.5 points, 11.8 rebounds and 9.8 assists and led the NBA in triple-doubles with 29.
"I would have still voted for Joel Embiid the MVP," Jackson said. "But with Giannis and Joker, second and third. They deserve that. Incredible year by him. He continues to make history. I own the mistake and I apologize."