The 20-year-old handed a letter to manager Jim Jeffries on Friday morning saying that he also wants to apologise to the Killie supporters.
The Scotland international is now looking forward to the season ahead with the Ayrshire side.
Rangers failed with repeated offers for Naismith over the summer, while Celtic enquired about a possible move.
However, Kilmarnock manager Jim Jefferies claimed the Scottish champions had failed to follow up a verbal offer.
Naismith submitted a written transfer request after becoming frustrated during the long-running transfer saga.
And Kilmarnock immediately put a £2m price-tag on their prize asset, who has three years of his contract to run.
Hibs and Hearts also approached Kilmarnock but neither Edinburgh club tabled a realistic offer.