Make you perfect - The apostle here does not affirm that they were then perfect, or that they would be in this life. The word used here - καταρτιζω katartizō - means to make fully ready; to put in full order; to make complete. The meaning here is, that Paul prayed that God would fully endow them with whatever grace was necessary to do his will and to keep his commandments; see the word explained in the notes on Hebrews 11:3. It is an appropriate prayer to be offered at all times, and by all who love the church, that God would make all his people perfectly qualified to do all his will.
Working in you - Margin, “Doing.” The idea here is, that the only hope that they would do the will of God was, that he would, by his own agency, cause them to do what was well-pleasing in his sight; compare notes on Philippians 2:12. It is not from any expectation that man would do it himself.
Through Jesus Christ - The idea is, that God does not directly, and by his own immediate agency, convert and sanctify the heart, but it is through the gospel of Christ, and all good influences on the soul must be expected through the Saviour.
To whom be glory forever and ever - That is, to Christ; for so the connection evidently demands. It is not uncommon for the apostle Paul to introduce doxologies in this way in the midst of a letter; see the notes, Romans 9:5. It was common among the Jews, as it is now in the writings and conversation of the Muslims, when the name of God was mentioned to accompany it with an expression of praise.