The 29-year-old, who missed over seven months after a cruciate ligament tear in 2024 and has suffered multiple knee and hamstring injuries this season, was forced off the pitch during City's 2-1 win over Arsenal on Sunday.
He missed City's 1-0 win over Burnley on Wednesday, which sent Guardiola's side to the top of the Premier League table, ahead of Arsenal on goals scored.
"He's better," Guardiola told reporters, but said the club would not rush the 2024 Ballon d'Or winner back to the field.
"We don't want to take a risk, because if he's injured, and we lose him the next five games. Rodri is so important."
Guardiola said rotation and recovery would be key in the final weeks of the season with City aiming to secure the English top-flight title along with the FA Cup as they look to complete a domestic treble, having won the League Cup last month.
"It was so demanding, the game against Arsenal, emotionally... the people were so tired, and they (took) a train for hours," the manager said.
"It's easier because of the fact we have a lot (of players) except Ruben (Dias), Rodri and Josko (Gvardiol), the rest are fit. But of course, you think it's the last effort.
"The question is will they be ready for tomorrow to play 90 minutes or maybe extra time, with a lot of players that have a lot of minutes in their legs. That is the question."
Guardiola said his players were happy to be leading the hunt for their seventh league title since 2017/18, but were focused on Saturday's game against Southampton.
"They are happy. The guys who don't play as much, not so much happy. We are just focusing on the game tomorrow," he said.
"Tomorrow will be a fantastic day. So many, many thoughts. Still I am in my mind and we'll see tomorrow."
