1. They, who are once effectually called, and regenerated, having a new heart, and a new spirit created in them, are further sanctified, really and personally, through the virtue of Christ’s death and resurrection (1 Cor. 6:11; Acts 20:32; Phil. 3:10; Rom. 6:5–6), by His Word and Spirit dwelling in them (John 17:17; Eph. 5:26; 2 Thess. 2:13): the dominion of the whole body of sin is destroyed (Rom. 6:6, 14), and the several lusts thereof are more and more weakened and mortified (Gal. 5:24; Rom. 8:13); and they more and more quickened and strengthened in all saving graces (Col. 1:11; Eph. 3:16–19), to the practice of true holiness, without which no man shall see the Lord (2 Cor. 7:1; Heb. 12:14).
Practical sanctification begins with regeneration. Those effectually called, born again by the Spirit, have as a result a new heart and spirit created within them. The new heart repented and believed, but the process of sanctification does not cease at this point. Through the virtue of the death and resurrection of Christ (i.e. the gospel), the individual believer is continually sanctified on a real and personal basis. The instrument of this sanctification is the Word of God and the indwelling Spirit. The result of the sanctifying work is that the dominion of the old man is utterly wasted and destroyed, the old man being understood as the rule or reign of sin. The lusts of remaining sin are gradually weakened and mortified, while the virtues and graces of true Christianity are gradually strengthened. The result is true holiness, lived out in the world—which, if not lived out, shows a complete lack of saving faith.
Notice that the Confession identifies effectual calling and regeneration as one kind of sanctification. Once they are effectually called and regenerated, they are “further” sanctified. The new heart believed, and that faith was the instrument of justification. But the new heart also continued to be a new heart, and continued to grow in holiness. In this sense, sanctification precedes justification, because it is a kind of sanctification that makes faith (the instrument of justification) possible.
2. This sanctification is throughout, in the whole man (1 Thess. 5:23); yet imperfect in this life, there abiding still some remnants of corruption in every part (1 John 1:10; Rom. 7:18, 23; Phil. 3:12); whence ariseth a continual and irreconcilable war, the flesh lusting against the Spirit, and the Spirit against the flesh (Gal. 5:17; 1 Pet. 2:11).
This sanctification is incomplete in one sense, but not in another. The “reach” of sanctifying impulses can touch every part of a man. But it does not touch every part so that this part becomes perfect or complete. No part of a man is untouched; no part of a man is completed. This incomplete sanctification brings about a state of war between the flesh on the one hand and the spirit on the other.
3. In which war, although the remaining corruption, for a time, may much prevail (Rom. 7:23); yet, through the continual supply of strength from the sanctifying Spirit of Christ, the regenerate part doth overcome (Rom. 6:14; 1 John 5:4; Eph. 4:15–16); and so, the saints grow in grace (2 Pet. 3:18; 2 Cor. 3:18), perfecting holiness in the fear of God (2 Cor. 7:1).
The flow of the battle may look grim for a time. True saints may appear to us as to have no grace, when in fact they are merely in a temporary backslidden state. That backslidden state may continue for a time, but in the truly regenerate, the Spirit never ceases His work, and the spiritual aspect of a man will overcome the fleshly aspect of a man. The result, considered overall, is that the saint grows in grace and perfects holiness in the fear of God.