City's youthful lineup, which included five full debutants and six teenage starters, were ruthlessly thrashed 5-1 at Stamford Bridge last weekend, as Pellegrini openly prioritised success in Europe.
But goals from Sergio Aguero, David Silva and Yaya Toure sealed an impressive win in Ukraine which delighted the Chilean, who revelled in seeing his plan come off.
"In this profession you always get criticism when you don't win, but I think it's important to take the right decision and think about a lot of things, about why you take this decision," he said.
"I always try to respect the competition. But in this case, having just 13 players, it was a key decision to rest the team that day.
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"Unfortunately we could not continue in the FA Cup, but I think it was important for the way we had to play this game [against Dynamo], with a lot of intensity."
Victory in Kiev has City standing on the brink of a first Champions League quarter-final appearance, progress Pellegrini is delighted to see his charges make after successive last-16 defeats to Barcelona.
"Each season we improve a little bit more," he said.
"The last two seasons we qualified for the last 16 and this season we made the important progress of winning the group, which was an improvement from last season.
"We now have the chance to arrive at the next stage and it's important if you can be among the best eight teams in Europe."