The 22-year-old played a vital role in the opening 45 minutes at the Etihad Stadium but left the field after Kyle Walker fired the hosts back into the lead after the break.
The Brazilian initially joined up with Benitez in January on loan from Chelsea, following a similar temporary spell with Watford, and returned to St James’ Park this season with on an option-to-buy deal.
“He had some headaches,” the Spaniard stated. “He was a little bit down.
“We could see at half time that he was not fine, but he wanted to continue. We could see he was not fine, though.”
Benitez also hailed the inspirational impact of goalkeeper Martin Dubravka after the Slovakia international made a series of excellent stops at the Etihad Stadium as his side went down fighting against their hosts.
Newcastle are still without a win four games into the new campaign, but Benitez singled out Dubravka as the kind of player who will be able to lift the side both on and off the field as the season picks up speed.
“When we signed him, we knew we were signing a good keeper,” the 58-year-old added. “Not too many people knew him, but we were following him for a while and we knew he was a good keeper.
“We also knew he had a very good mentality and was a good professional.”
Dubravka initially arrived at St James’ Park on a loan deal from Sparta Prague during the January transfer window, before completing a permanent move to Tyneside at the conclusion of the 2017-18 campaign for a fee of £4.5m ($5.8m).
“He has been very good in the dressing room,” Benitez further elaborated. “In these type of games, his contribution is very important for us.
“When you have teams that are attacking so much, the keeper is the one that can give confidence to the defenders and he is doing well.”
Newcastle next play Arsenal on September 15 following the conclusion of the international break.