Deans rested a number of star performers like Quade Cooper and James Horwill, giving some fringe players a chance to push their claims for World Cup selection.
But the decision backfired as his side were outplayed and out-muscled by the tiny pacific nation at ANZ Stadium on Sunday.
It was a dismal start to the Wallabies' season, which continues with a Tri Nations opener against South Africa this weekend and one eye on the World Cup starting in New Zealand in just two months.
But Deans stood by his team selection on Monday, insisting it was simply performance and not personnel that led to the defeat.
When asked if he should have picked his best available side with the World Cup so close, Deans said: "We're damned if we did and damned if we didn't.
"We've got a whole campaign to run and a six day turnaround before playing South Africa in our first Tri Nations outing this weekend.
"The Reds players didn't join us until late Monday and clearly needed a break.
"They'd come off a huge Super Rugby campaign and hadn't trained with us.
"Sure we could have thrown them out there but the outcome may not have been much different and we would have been doubly worse off.
"We've been able to give some of those blokes time to recover, recuperate and to look forward."
Deans admitted the loss to Samoa was a timely wake-up call for his squad ahead of the World Cup, but scoffed at suggestions his players were arrogant and failed to show their opponents enough respect.
"It's an easy suggestion to make under the circumstances but we just didn't play well," he said.
"None of us are comfortable with that, but a suggestion (our performance was) based on a lack of respect is nonsense.
"We talked not only internally but externally pre-game about the capabilities of the Samoan side.
"This was their World Cup combination chosen from their best players across the globe.
"As we saw they are a good side... they've got some proud history behind them and we didn't underestimate them."
The Wallabies should be boosted by the return of David Pocock (foot) for the clash with the Springboks on Saturday, but James O'Connor is still a doubt with a hamstring injury.
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