In its literal sense, a yardstick is a measuring rod a yard long, typically divided into inches. But more broadly, it can also be defined as a standard for making a critical judgment or comparison. For example:
Some feel that test scores aren't an adequate yardstick for judging a student's ability.
Ratings are the yardstick by which TV shows are evaluated by networks.
The sentence also states that 'time' will be using this yardstick, which may add a layer of confusion. 'time' is used to establish the when of our judgement - i.e we will be judged in the future. It's similar in concept to the expression 'history will be my judge' - when people in the future look back on my actions now (which will be their history), they will judge whether I was right or wrong.
Therefore, in the sentence you have given, Pope Francis is stating that how we measure others, is how we ourselves will be measured by others, when, in the future, people look back on this moment in time. A similar expression would be 'what goes around, comes around'.