These sections of the novel are different, but not necessarily in tone. The entire novel is comical, farcical, whimsical, and full of adventure. Throughout the novel, the characters fail to appropriately or fully assess reality and deal instead in some semblance of fantasy.
The change that takes place in the last section of the novel has to do with Huck Finn's awareness of his own folly and his willingness to make this awareness known in the narrative.
We can see a similar tone in Huck's narrative in two particular episodes. Early in the novel Huck watches Tom Sawyer and other townspeople as they fire cannons from a boat while searching for Huck's supposedly dead body.
When the boat comes close, Huck is almost killed by a cannon blast:
Then the captain sung out: "Stand away!" and the cannon let off such a blast right before me tht it made me deef with the noise and pretty near blind with the smoke, and I judged I was gone.
The irony of this situation (Huck is nearly killed while watching people search for his dead body) is parallel to that of one of the book's final episodes.
When Tom awakes after days of sleep after he is shot, he announces that Jim is a free man and has been free since Tom arrived at the Phelps house.
All the antics and adventures performed to free Jim from bondage were completely unnecessary. Jim was already, ironically, free. The connection between these episodes demonstrates a continuity of tone through the novel. The text is, for the most part, always humorous, fast-paced, and dependent on folly and fraud for its action.
Tom Sawyer continues this folly and fraud in the final section of the novel.
In the last third of the book, Huck defers to Tom Sawyer, whose outlandish schemes to free Jim direct the action. Huck is no longer in charge, and his moral quest appears to have been abandoned.
What separates the latter section from the earlier one is Huck's attitude. Huck decides to go against society's code of moral law and to free his friend Jim if he can before Tom Sawyer arrives. His major conflict has been resolved, it would seem. However, Tom Sawyer is a subtle stand-in for the society that Huck has attempted to free himself from, morally speaking, and the dominance of Huck's conscience continues through Tom.
In this section, Huck does not rebel beyond a certain point against Tom and the society (moral authority) he represents. Instead, he demonstrates an ambivalence toward this authority. This ambivalence is new. Where Huck once agonized over right and wrong, he now muses on the folly of accepted wisdom.