Bernardo Silva's opener for City was canceled out by Iliman Ndiaye for Everton, leaving the hosts with one win in the past 13 games.
“Nathan made an incredible effort,” said Guardiola, with Ake having only just returned from a hamstring injury. “Thank you so much for the effort he has done.
“He needs a little more but for the circumstances we have, he made an effort. I said when you feel fatigue, let us know.”
On the latest players missing, Guardiola said: “Kyle (Walker) was flu, a virus and Jack yesterday in training felt something muscular – a similar reason to why Ederson doesn’t feel good.”
He continued: “We shot I don’t know how many shots.
“The first half was brilliant and the first 10 or 15 minutes of the second half was really good.
“The first time they arrived they scored a goal. At the end, there were transitions and we controlled to avoid the defeat but we analyse the result because we are not happy.
“The performance and the way the guys have done in the situation were brilliant.
“We didn’t score the goals we need but there are games where I don’t like what I see: today that was not the case.”