The publisher merged the ad sales teams of the two titles in 2008 as part of a strategy to sell them together.
David Wilcox has been named the sales director of The Sun and Tammy Willson has been appointed the sales director of The Times and The Sunday Times.
They both report to the chief commercial officer, Dominic Carter, who continues to oversee a single team.
The Sun’s website has recently gone free to reach a mass audience, while The Times and The Sunday Times use a paywall.
It comes as News UK is axing up to 100 roles. But it is thought that only half are in commercial and new jobs are also being created.
As part of the new sales structure, The Sun and The Times will each have its own digital ad team and agency relationship team because the audience proposition for each title is now "very different", Carter said.
The magazine supplements such as The Sun’s TV magazine and the Sunday Times’ Style and Culture will also each have dedicated ad teams.
Carter said "it made sense at the time" in 2008 when the papers’ ad sales teams were merged in a single operation with no "title-specific" sales directors or representatives, but "the world has changed", particularly as The Sun and The Times now have different business models.
"I don’t think you can have enough depth, if you work across all the titles. You need to describe your audiences and your titles to clients. People want to know what the likelihood is of reaching a Sun reader or a Times reader. A client might be going for mass market or quality – you need that expertise."
He dismissed suggestions that News UK is going back to a previous era where each title was sold separately. "It’s not a retro thing," he insisted.
News UK continues to run some of its ad sales centrally. It has a client team, which handles brands, and a category team, which looks after different categories, that operate across all titles.
Carter said his priority was "understanding the objective of the client". He went on: "I’m trying to shift the way we do business. We must talk more to clients. We can’t over-rely on agencies. We’ve still got to talk to agencies, but they’re under pressure."
He would not comment on any job cuts but said: "Sometimes when you want to change things, you have bring in new people. I want to accelerate that change."
Carter’s move to split The Sun and The Times contrasts with some other rival newspaper groups that have a unified sales team.
He said News UK’s stable of titles meant it needed to be run differently from Mail Brands, the ad sales arm of the Daily Mail, "where you just sell the Mail", and Telegraph Media Group, "where you just sell the Telegraph".