It is fairly common to see people making the sign of the cross when the priest says the words, “May almighty God have mercy on us, forgive us our sins, and bring us to everlasting life. Amen.” Yet, that sign of the cross is not indicated in the rubrics of the Mass and never has been in the history of the Novus Ordo (i.e. since 1969). So where does it come from?
I believe that this is a carryover from the older form of the Mass — what we now call the Extraordinary Form. When the priest and servers (or deacons) are saying the “Prayers at the Foot of the Altar” in the old Mass, it is then that the “penitential rite” takes place. The priest recites the confiteor prayer (I Confess); then the servers or deacons do so. After they have done so, the priest says:
Misereatur vestri omnipotens Deus et, dimissis peccatis vestris, perducat vos ad vitam aeternam.
May almighty God have mercy on you, forgive you your sins, and lead you to everlasting life. (The translation is slightly loose, to make it match up better with what we currently say.)
At that point, however, the priest and ministers do not make any gestures like signs of the cross. It is immediately after that they do so. The next thing the priest says is:
Indulgentiam, + absolutionem, et remissionem peccatorum nostrorum tribuat nobis omnipotens et misericors Dominus.
May the + almighty and merciful God grant us pardon, absolution, and remission of our sins.
It is while the priest is saying those last words that he signs himself.
The “Misereatur vestri” prayer was brought into the new Mass, but the one that immediately follows it, “Indulgentiam, absolutionem, et remissionem” was not. Yet — I opine — the gesture that accompanied it was. Not officially, but through popular piety. Many people remembered it and got in the habit of making the sign of the cross when the priest recited the so-called “absolution” in the new penitential rite.
So this gesture is not in the rubrics of the “new Mass”; it doesn’t even quite go with the prayer that it accompanies, historically speaking. But I would say that it is meaningful to many, and a harmless thing to do.