The Blues drew 1-1 with the Magpies before winning 4-2 on penalties on Tuesday night to reach the semi-finals of the Carabao Cup.
Chelsea fans were confused in the 32nd minute though as Pochettino brought off midfielder Fernandez for striker Armando Broja.
It seemed like a tactical decision at first but he made his way straight down the tunnel, and the Blues' boss explained after the match that his fellow Argentine was unwell.
"He felt sick," said Pochettino. "He didn't feel well before the game and then when he started to play, it wasn't going well. He asked to come out because he wasn't feeling well.
"He was a little bit sick before the game. He tried, he wanted to play, see if it goes well but it goes not so well and that is why [he looked upset]."
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Fernandez cut an emotional figure at full-time too despite the win, with Pochettino and Reece James spotted consoling him.
Argentine journalist Gaston Edul has reported that the 22-year-old is suffering from the 'beginning of pubalgia', with 'rest or treatment' needed to recover.
Pubalgia is a chronic groin lesion, with Lionel Messi speaking on the injury in 2019 and what it's like to deal with.
"Pubalgia is complicated. I suffer from it for a while now, I do little training and I can not play all the games," Messi said.
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"It is not a problem that can be solved overnight. I feel better now, but I still have not recovered and I still need treatment."
Fernandez, who has featured in all but one of Chelsea's 21 matches this season, could now be set for a spell on the sidelines.
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His substitution came 16 minutes after Callum Wilson opened the scoring for Newcastle following some poor Blues defending.
Chelsea looked as though they were about to be knocked out of the Carabao Cup but Mykhailo Mudryk scored a stoppage-time equaliser.
Penalties were therefore required and Pochettino's side won 4-2 in the shootout, with Djordje Petrovic making the deciding save.