Managing a calf complaint, Rose was a notable absentee in the newly-minted premiers' 4-0 F3 derby win over Central Coast on Anzac Day.
But the 26-year-old's services weren't needed, with the home side scoring three first-half goals within 23 minutes at McDonald Jones Stadium.
The Jets will enjoy a bye weekend before hosting a two-legged semi-final as they eye a historic domestic treble.
"Yeah, it was the right decision," Milligan said of managing Rose.
"We have a fantastic medical staff. They made that decision.
"All year, I have to trust what they say and the players trust what they say.
"It was in the best interest, first and foremost, of 'Rosie'."
Rose has been instrumental for the Jets and has scored eight goals, just one behind club-leader Clayton Taylor.
The former Macarthur FC player has yet to win a league championship and will leave Newcastle to join Scottish Premiership side Dundee United on a two-year deal at the end of the finals.
Resting Rose wasn't the only precautionary measure, with winger Eli Adams sending a scare through the Jets camp in the 53rd minute.
Adams hurt his right ankle after his foot was caught while trying to fend off Mariners left-back Lucas Mauragis.
The 24-year-old scored a header on 44 minutes, joining Will Dobson, Taylor and Kota Mizunama on the scoresheet.
Adams was then substituted off in the 55th minute.
"I knew Eli was OK. Eli gave me a little thumbs-up," Milligan said.
Milligan was adamant there was no pressure felt to complete the premiership-championship double, alongside their Australia Cup triumph from last October.
No side has won that treble in one season before.
Central Coast were the last side to pull off the league double, which completed an international treble with their AFC Cup title.
"Now we start to see how brave teams really are in finals," Milligan said.
"I know one thing for sure: I've got a very, very brave group of boys who are willing to execute what we need no matter the circumstance or the situation.
"There is no pressure on this playing group because they execute every single day."