The former couple, who announced their separation on Friday (June 29), are said to have agreed during a "brief and civil" conversation that their 6-year-old daughter has to be their priority.
"It was brief and very civil," a source told The Mirror. "Both appreciate that things can't descend into all-out war.
"They are trying to be adult about things, not least because there are children to think about.
"Tom and Suri have talked several times since the split so it was only a matter of time before Katie spoke to Tom herself."
An insider added that Cruise is heartbroken about only being able to speak to Suri on the phone.
"It's not ideal but as long as Tom gets to speak to Suri he doesn't care," they said.
"It breaks his heart to have to speak to her on the phone - and not face to face - but hopefully that will change soon."
The actors' different approaches to parenting and Holmes's fears about Suri being forced to adopt Scientology are believed to have contributed to their split.
Photo gallery - Katie Holmes and Suri out and about after divorce: