How did Mr. Darcy justify his behavior toward Jane and Mr. Wickham?

Unraveling Mr. Darcy’s character in Jane Austen’s Pride and Prejudice is a delightful party game that has intrigued readers for centuries. To answer the first part of your question, Mr. Darcy justifies his prejudice towards Jane Bennet by telling Elizabeth that he did not believe she showed any partiality for Mr. Bingley and that he did not believe she liked him better than any other gentleman she danced with at the Netherfield ball. Unaware that many young ladies were advised to be careful in their demeanor towards young men, Mr. Darcy is concerned that his friend may be wasting his affection on a woman who does not appear to care for him and advises Bingley to leave the neighborhood and return to London. Many readers believe that Mr. Darcy did this heartbreaking deed hoping that Bingley would develop affections for his sister, Miss Georgiana, but Austen’s plot does not twist that way. That said, to answer the second part of your question regarding Mr. Darcy’s behavior towards Mr. Wickham, his justifications are on more solid ground. In Mr. Darcy’s view, Mr. Wickham is a ne’er do well in lamb’s clothing. Lazy and irresponsible, Wickham has abused the trust of the Darcy family in many ways: he squandered the inheritance that he extorted from Mr. Darcy and eloped with Miss Georgiana when she was just 15. Luckily, Mr. Darcy was able to save his sister from such a loathsome alliance. Mr. Darcy’s pride keeps him from confronting Wickham’s lies about the past until he realizes it has cost him the favor of Elizabeth, the woman he loves. It is only in a letter from Mr. Darcy to Elizabeth following her rejection of his proposal of marriage that the reader learns the true extent of Wickham’s deceit and depravity.

Mr. Darcy's justifications are two-fold, as his actions toward Mr. Wickham and toward Jane spring from separate motivations. Still, they share a similar thread, as each reflects Mr. Darcy's judgement of character.
As Mr. Darcy explains, he warns Mr. Bingley away from Jane because he believes that she does not return Bingley's affections. (Ironically, Darcy later fights his own admiration of Elizabeth, who truly does not reciprocate, though he is mistaken concerning Jane's feelings.) In fact, undemonstrative Jane is very much in love with Mr. Darcy's good friend but is far too meek to declare her love. To be certain, Mr. Darcy also prevents Mr. Bingley from pursuing Jane because of her social position and family, but this is paired with his concern that Jane is only flirting with Mr. Bingley.
While Mr. Darcy misjudges Jane's character when he separates her from Mr. Bingley, Mr. Darcy is astute in his understanding of Mr. Wickham. As Mr. Wickham's past behavior reveals, the man is an untrustworthy scoundrel. Mr. Darcy treated him very kindly, all things considered, and respected his own father's wishes regarding Wickham. Lizzie misjudges Mr. Darcy, at first, by believing Mr. Wickham instead.