NBA commissioner David Stern fined the Spurs $250,000 for the move, saying it was an unreasonable approach to resting players.
Popovich said Stern's fine did not have an impact on his decision this time around.
"This is a little different. This one, everybody is healthy," Popovich said. "It's not about rest, it's about health and about safety. Rest comes into it a little later in the season."
Popovich pointed out that when he made the decision for the Miami game it was at the end of a stretch when the Spurs had played 10 of 13 games on the road and they had another game two days later at home. The Spurs, who have won seven games in a row, have two days off after playing the Knicks.
"For us, being older, it is about doing what you have to do at the beginning of the year so they're there at the end," Popovich said.