Having reacted angrily after he was taken off in a Champions League clash with Salzburg last week, Saul had to settle for a place on the bench in the Madrid derby.
The 26-year-old came on with an hour played, though could not help Atleti avoid a 2-0 defeat to their city rivals.
Saul returned to Atleti's starting XI as captain on Wednesday, playing on the right as Simeone's team cruised to a 3-0 Copa del Rey win over minnows Cardassar.
It was a quiet display from the versatile midfielder, with Geoffrey Kondogbia and Lucas Torreira dominating the centre of the pitch for the visitors.
Saul attempted 56 passes, fewer than all but two Atleti outfielders from the starting line-up, completing 42 of them (75 per cent).
He lost possession 20 times – a team-high and second only to Cardassar goalkeeper Angel Pedro Sanchez Marin, and did not make any key passes.
Defensively, Saul also lacked his usual efficiency, regaining possession on only three occasions, seven fewer than Kondogbia and six less than Torreira, while he also failed to make a tackle, conceding one foul for which he was booked.
From eight LaLiga appearances so far this season, Saul is yet to score or provide an assist. Last season, he netted six times in the league, while creating 15 chances in total.
Asked about Saul's display, Simeone told reporters: "I was pretty clear yesterday. He is very important to us, he has always given us a lot from day one and the players go through different moments.
"Saul knows that he has to improve, he works for it and we are waiting for him to give us a lot of things as he has always given us."
While Saul struggled out on the flank, Kondogbia and Torreira impressed their coach.
"I really liked both of them," he added. "They occupied the width of the pitch, they worked very well in circulation, Kondogbia tried the shot, Lucas had very good passes and it is a very good performance for both of us, which helps us and we need everyone."