Leam Richardson defended the decision to ring the changes as Pompey fell to a final-day defeat.
And the Blues assistant manager insisted travelling to Plymouth Argyle for the second leg of the play-offs is of little consequence.
That is what Paul Cook’s side will be doing next Sunday after Saturday’s 2-1 loss to champions Northampton Town at Fratton Park.
The Blues ended their regular League Two campaign with defeat to the Cobblers in front of a crowd of 18,746.
Cook made changes for the game with five switches from the team who picked up a win at Hartlepool.
Enda Stevens, Danny Hollands, Michael Doyle and Christian Burgess were rested with a top-seven spot assured.
That led to minutes for the likes of youngsters Jack Whatmough, Ben Tollitt, Adam May and Brandon Haunstrup.
The result went against Pompey but Richardson was adamant shaking up their options was the right thing to do.
He feels protecting the players for Plymouth is of paramount importance.
Richardson said: ‘The manager made the decision not to put certain players on the pitch.
‘Our fight is Thursday and Sunday. We gave up this fight against Northampton by not winning enough home games.
‘We thought it was going to be a big game but we gave up that right.
‘So it was irrelevant as a result, so lads not playing was part and parcel of that.
‘We ended up with a couple on yellow cards and you know the niggles we have.
‘So you are throwing a team around your head for Thursday after 70 minutes.
‘With Gaz (Roberts) it’s important he plays. He’s been stop-start this year.
‘When he plays you see his quality and how we’ve missed it when he’s not there.
‘So we had to keep him going and match fit. That was the thinking behind that.
‘We have to do what is right for the team rather than the individual.
‘It was important we came through the game.’
The loss combined with Plymouth’s comprehensive 5-0 win over Hartlepool means Derek Adams’ side rose above Pompey in the League Two table after the final round of fixtures.
That means the Pilgrims will come to Fratton Park on Thursday before the return at Home Park on Sunday.
Having the home leg second is viewed as an advantage but with Pompey’s record better on the road, Richardson doesn’t see that as the case.
He said: ‘People will argue it’s better to play at home second but we haven’t had a penalty at home all season.
‘We haven’t had decisions, so why people think it’s automatically better to play at home second is beyond me. I don’t know why.
‘I have got no preference. You’ve got 180 minutes to beat a team.’