The 'Midnight Sky' actor and director admitted he was secretly panicked with his leading lady called to reveal she was expecting her first baby, who was born in April last year.
Speaking to The Hollywood Reporter magazine, Clooney said: "We're in Iceland on a glacier and I got a call from Felicity and she says, 'Well, I'm pregnant'.
"I knew how to answer that, which is, 'Congratulations'. But if you saw my face, I'm like, 'Holy s***'.
"We started to try to shoot around it, which is always a mistake, because you can't shoot around it. People know when you're hiding things."
Instead, the 59-year-old star decided to adapt the script - which is based on the novel 'Good Morning, Midnight' by Lily Brooks-Dalton - and introduce a new element to Jones' character.
He added: "So we just looked at it and said, 'Look, they've been in space for two years, people have sex. It's like going on location'.
"I just thought, like Fran [McDormand] in 'Fargo', women every single day are pregnant, going to work and doing their job, and why not in space and why not just deal with it?"
For Clooney, directing and acting in the same project gave its own challenges, particularly when his collaborator Grant Heslov got involved.
He explained: "I have my best buddy and producing pal for 40 years, Grant, who sits behind a monitor, and you want to do fewer takes on yourself than you want to do on other people, because you look like a schmuck otherwise.
"You do a couple of takes and you go... 'Yeah, that's fine'. And then Grant will stick his head out and go, 'Do another take, please'. 'Oh, OK. All right.' "