Anderson looked fit in his return to the team in their 216-run hammering of a local side in Canberra on Monday, but sat out Wednesday's win over the Prime Minister's XI.
Morgan said the decision was made to rest their spearhead to give him the best possible chance to play in Friday's tri-series opener.
"It was more managing his workload coming back from injury," Morgan told reporters. "We decided that he wouldn't be able to play three games in a week and obviously the most important game is tomorrow.
Anderson was put through a full practice session Thursday with Morgan saying "we'll see how he pulls up tomorrow morning".
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He added that Anderson was the only injury concern heading into the one-day international.
"Everybody else is, to my knowledge, at the moment fit for selection."
Morgan praised Ian Bell's 187-run knock against the Prime Minister's XI, the highest innings by an England batsman in a competitive 50-over match, and said it epitomised the ruthlessness his side needed to succeed.
"It'll be nice to be sitting here at the end of this series with some silverware and very confident in where we're going as a side," Morgan said.
"I know throughout this series it might throw up a couple of things because Australia can be a difficult place to tour, a difficult place to adapt to conditions, but I certainly think that we're one of the sides that finds it a lot easier to adapt.
"They are conditions that suit our game and we proved that a bit yesterday. Mindset and method wise, we're in a good place -- particularly with our batting.