He kept pressing, growing in influence as Anderlecht exhausted, until the pressure he continued to provide at No.10 paved the way for Rashford to score a dramatic late victor to send United through to the semis.
But the 3-2 aggregate success came at a price, with Ibrahimovic and Rojo both seemingly set for extended spells on the sideline after being taken off.
United's record goalscorer Wayne Rooney made his return against Anderlecht, taking his place on the bench after missing four games with an ankle injury, but Mourinho suggested the club captain is not yet ready to play.
Mourinho last week said the England centre-backs were out until mid-May, but suggested after the Anderlecht win that they need to be "brave".More news: Cristiano Ronaldo Pleas With Real Madrid Fans Not To Boo Him
The Manchester United manager said the severity of the injuries is likely to be known in "a couple of days".
United find out their semi-final opponents in Friday's draw, with Ajax, Celta Vigo or Lyon lying in wait.
Both players will be bemused by his comments, with Smalling already having been criticised by the Portuguese for pulling out of a game at Swansea City when he had broken a toe, earlier this season.
"But the news is fairly negative I think".More news: Michigan State DE Auston Robertson Charged with Criminal Sexual Conduct
"He could by age, so when you reach a certain level - and he's reached that level for a long time - I don't think it makes sense, but the power is in their hands".
"We can not do miracles".
"But he was not scoring a goal since September and because of his mentality, because of what he gives us, even if he isn't scoring goals I kept relying on him". There are no miracles but with special spirit you can sooner than expected. "So instead of coming mid-May you can come beginning May - this kind of acceleration of the process", he said.
He said: "I'm relieved, relieved, hard game".More news: BJP wins Latur, Congress gains in Parbhani
"I am exhausted. I imagine the players are more exhausted than me".
- Injury won't impact Wilshere's Arsenal future, says Wenger
- Father of Tennessee girl says he is overjoyed
- Jose Mourinho fears worst after Ibrahimovic and Rojo Injuries sour European win
- Oil prices flatten as rise in United States production weighs
- Lingard: Herrera was key to Chelsea win
- Bill O'Reilly to get payout up to $25 million
- Comedian Don Rickles dies at 90
- Nashville Predators complete sweep of Chicago Blackhawks
- Raheel Sharif leaves for Saudi to lead Islamic military alliance
- Sanders Urges Party To Go Beyond Comfort Zone