Objection 1. It would seem that we ought not to pray for our enemies. According to Romans 15:4, "what things soever were written, were written for our learning." Now Holy Writ contains many imprecations against enemies; thus it is written (Psalm 6:11): "Let all my enemies be ashamed and be... troubled, let them be ashamed and be troubled very speedily [Vulgate: 'Let them be turned back and be ashamed.']." Therefore we too should pray against rather than for our enemies.
Objection 2. Further, to be revenged on one's enemies is harmful to them. But holy men seek vengeance of their enemies according to Apocalypse 6:10, "How long... dost Thou not... revenge our blood on them that dwell on earth?" Wherefore they rejoice in being revenged on their enemies, according to Psalm 57:11, "The just shall rejoice when he shall see the revenge." Therefore we should not pray for our enemies, but against them.
Objection 3. Further, man's deed should not be contrary to his prayer. Now sometimes men lawfully attack their enemies, else all wars would be unlawful, which is opposed to what we have said above (Question 40, Article 1). Therefore we should not pray for our enemies.
On the contrary, It is written (Matthew 5:44): "Pray for them that persecute and calumniate you."
I answer that, To pray for another is an act of charity, as stated above (Article 7). Wherefore we are bound to pray for our enemies in the same manner as we are bound to love them. Now it was explained above in the treatise on charity (25, 8,9), how we are bound to love our enemies, namely, that we must love in them their nature, not their sin. and that to love our enemies in general is a matter of precept, while to love them in the individual is not a matter of precept, except in the preparedness of the mind, so that a man must be prepared to love his enemy even in the individual and to help him in a case of necessity, or if his enemy should beg his forgiveness. But to love one's enemies absolutely in the individual, and to assist them, is an act of perfection.
In like manner it is a matter of obligation that we should not exclude our enemies from the general prayers which we offer up for others: but it is a matter of perfection, and not of obligation, to pray for them individually, except in certain special cases.
Reply to Objection 1. The imprecations contained in Holy Writ may be understood in four ways. First, according to the custom of the prophets "to foretell the future under the veil of an imprecation," as Augustine states [De Serm. Dom. in Monte i, 21. Secondly, in the sense that certain temporal evils are sometimes inflicted by God on the wicked for their correction. Thirdly, because they are understood to be pronounced, not against the men themselves, but against the kingdom of sin, with the purpose, to wit, of destroying sin by the correction of men. Fourthly, by way of conformity of our will to the Divine justice with regard to the damnation of those who are obstinate in sin.
Reply to Objection 2. As Augustine states in the same book (De Serm. Dom. in Monte i, 22), "the martyrs' vengeance is the overthrow of the kingdom of sin, because they suffered so much while it reigned": or as he says again (QQ. Vet. et Nov. Test. lxviii), "their prayer for vengeance is expressed not in words but in their minds, even as the blood of Abel cried from the earth." They rejoice in vengeance not for its own sake, but for the sake of Divine justice.
Reply to Objection 3. It is lawful to attack one's enemies, that they may be restrained from sin: and this is for their own good and for the good of others. Consequently it is even lawful in praying to ask that temporal evils be inflicted on our enemies in order that they may mend their ways. Thus prayer and deed will not be contrary to one another.
Source: Summa Theologica (New Advent)