Foden, who was one of only four outfield players to remain in the starting line-up from Sunday’s 1-0 win over Chelsea, claimed his 15th goal of the season to open the scoring at the Amex Stadium, but was replaced five minutes into the second half.
Stones was also replaced late in the second half with fellow central defenders Manuel Akanji, Aymeric Laporte, Ruben Dias and Nathan Ake missing the trip to the South Coast along with Jack Grealish.
“Phil had a knock in the first half and problems in his leg and the doctor told me that in this position, it is dangerous so we don’t take a risk but Phil was exceptional in the first half,” Guardiola said.
“John felt a little tight but he didn’t feel anything and is fine, he told me, but we didn’t want to take a risk because we had just one central defender with John.
“The others are injured so hopefully they can recover as soon as possible.”
Guardiola said that several players have niggles which the City physios are helping the players to recover from after a hectic schedule over recent weeks.
“We have an incredible staff with our physios - without them, it would not be possible,” he added.
“Because we sustained no injuries for a long time I don’t know what happend but the moment we get near the Champions League final, four or five players get little niggles - important ones and we have to recover them.
“We had to play a strong team against Brighton because you can play 90 minutes in your own box and I didn’t want that.”
Meanwhile, Guardiola was left frustrated by the VAR check that led to Erling Haaland‘s late strike being disallowed.
The City striker was adjudged to have pulled Levi Colwill’s shirt before heading in Cole Palmer‘s cross for what would have been his 53rd goal of the season.
“He has bruises all over his body after the game,” Guardiola said. “If his action is a foul in the goal that is disallowed then every action to him is a foul but it never happens.
“It’s a goal because he’s bigger. He’s stronger and he won the position and it was an incredible action from Cole Palmer and the goal should have been given.
“But the point we won on the pitch belongs to us, no one gave us anything.”
