I work at an institution and the owner sometimes unjustly deducts from the workers' pay. I can prevent such injustice without the knowledge of the institution's owner but is this permissible?

All perfect praise be to Allaah, the Lord of the worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad, sallallaahu ‘alayhi wa sallam, is His slave and messenger.

It is an individual obligation on any Muslim to undo injustice that cannot be undone except by him, unless a greater harm will follow. That is an act of true injustice. Being certain of it, a person has to do his best to obviate or undo it.

The Prophet was reported to have ordered every Muslim to support his fellow Muslim, whether he is doing wrong or wronged. In the first case supporting him can be achieved by preventing him from doing injustice. Al-Baraa’ ibn ‘Aazib also narrated that the Prophet ordered the companions to support every wronged person. [Al-Bukhari] 

Undoing an act of injustice or preventing an expected one is not conditional on the wrong doer's permission or knowledge, when it is likely to hinder the process of establishing justice. Many rights are restored without the perpetrator’s knowledge. Allaah Says (what means): {So whoever has assaulted you, then assault him in the same way that he has assaulted you.}[Quran 2:194]

Al-Bukhari mentioned that the wronged person is permitted to restore his rights, when possible, from the wrong doer's money, referring to the verse of Quran that reads (what means): {And if you punish [an enemy, O believers], punish with an equivalent of that with which you were harmed.}[Quran 16:126]

Hind bint ‘Utbah narrated that the Prophet had permitted her to take from her miserly husband, without his knowledge, the amount of money that would be sufficient for her and her children. [Al-Bukhari]

The above Hadeeth narrations indicate the permissibility of restoring a person’s rights without the knowledge or permission of the one who has wrongly taken them.