The Argentine returned to the match-day squad last weekend after spending seven months on the sidelines with a knee ligament injury.
He was handed a start against FC Basel on Wednesday and provided the one positive in what was an otherwise poor showing with a composed, powerful display at the back.
But Mourinho, speaking ahead of the clash with Brighton, hinted towards protecting the defender from too many minutes too soon on Saturday.
“The injury is gone, but after playing his first match back, maybe he feels it a little bit,” he said.
Phil Jones and Eric Bailly will not make it back in time for the visit of Chris Hughton’s side but Mourinho is right to cast caution over giving Rojo two starts in four days so soon after recovering from a serious injury. His accomplished performance in Switzerland suggested otherwise, but he will need time before returning to full sharpness.
In the meantime, however, supporters will hope to see Victor Lindelof, who made his first Premier League start against Newcastle last weekend, handed another chance to continue his development under Mourinho following a difficult start to life at Old Trafford.