The European champions struggled to break down minnows Andorra in Saturday's World Cup qualifier and it was left to their star man to rescue all three points from the bench.
Ronaldo, one booking away from a suspension, did not take long to open the scoring after being brought on at the interval, before sending in a dangerous cross for his side's killer second in the 2-0 win.
Asked about the Real Madrid star's absence from the off, Santos told RTP: "I thought [about it] a lot. I thought, well, Ronaldo did not train 100% in two of the days of work.
"There were many factors that led to this decision. Games are complicated, I tried to manage and do what was best. Whether it was questionable or not... we ended up winning and that's what matters."
Ronaldo now has 15 goals in the ongoing World Cup 2018 qualifying campaign, which continues with a must-win match at home to Switzerland on Tuesday night.