بسم الله الرحمن الرحيم
This becomes clear when one understands the meaning of (سبحانك), “glory be to You; far removed are You from any imperfection” for this statement comprises exaltation of the Lord as well as absolving Him of all deficiency. The situation that Yunus found himself in demanded that Allah be absolved of oppression and that He be absolved of punishing without cause, therefore he said, ‘You are Holy, absolved of oppressing me or punishing me without cause, rather I am the oppressor who has oppressed himself.’ Allah, Exalted is He, says,
وَمَا ظَلَمْنَاهُمْ وَلَـٰكِن كَانُوا أَنفُسَهُمْ يَظْلِمُونَ
«We did not wrong them; rather they wronged themselves»[Surah an-Nahl 16:118]
وَمَا ظَلَمْنَاهُمْ وَلَـٰكِن ظَلَمُوا أَنفُسَهُمْ
«We did not wrong them; rather wronged themselves» [Surah Hud 11:101]
وَمَا ظَلَمْنَاهُمْ وَلَـٰكِن كَانُوا هُمُ الظَّالِمِينَ
«We have not wronged them; it was they who were the wrongdoers»
رَبَّنَا ظَلَمْنَا أَنفُسَنَا
«Our Lord! We have wronged ourselves» [Surah Al-Araf 7:23]
Similarly the Prophet صلى الله عليه وسلم said in the sahih hadith reported by Muslim concerning the opening supplication in prayer,
اللَّهُمَّ أَنْتَ الْمَلِكُ، لاَ إِلَهَ إِلاَّ أَنْتَ، أَنْتَ رَبِّي وَأَنَا عَبْدُكَ، ظَلَمْتُ نَفْسِي، وَاعْتَرَفْتُ بِذَنْبِي، فَاغْفِرْ لِي ذُنُوبِي جَمِيعًا، إِنَّهُ لاَ يَغْفِرُ الذُّنُوبَ إِلاَّ أَنْتَ
0 Allah! You are the King, there is none worthy of worship besides You; You are my Lord and I am Your servant, I have wronged my soul and I acknowledge my sin, so forgive me all my sins for indeed none forgives sins save You. Muslim [#771] and Abu Dawud [#760].
Bukhari records the hadith,
The master of asking for forgiveness [is the supplication],
اللَّهُمَّ أَنْتَ رَبِّي لا إِلَهَ إِلا أَنْتَ خَلَقْتَنِي وَأَنَا عَبْدُكَ وَأَنَا عَلَى عَهْدِكَ وَوَعْدِكَ مَا اسْتَطَعْتُ أَعُوذُ بِكَ مِنْ شَرِّ مَا صَنَعْتُ أَبُوءُ لَكَ بِنِعْمَتِكَ عَلَيَّ وَأَبُوءُ لَكَ بِذَنْبِي فَاغْفِرْ لِي فَإِنَّهُ لا يَغْفِرُ الذُّنُوبَ إِلا أَنْتَ
`0 Allah! You are my Lord, there is none worthy of worship save You. You created me and I am Your servant, I am trying to fulfill Your agreement and promise to the best of my ability. I take refuge with You from the evil I have wrought, I acknowledge Your favours to me and I confess my sin, so forgive me for none forgives sins save You.’
Whoever says this supplication with certainty when he awakes in the morning and dies during that day, he will enter Paradise. Whoever says this supplication with certainty when he lies down to sleep in the evening and dies during that night, he will enter Paradise.’ Bukhari [#6306] and an-Nasal [8/279].
Hence it is upon the servant to acknowledge the justice of Allah and His benevolence; He does not oppress man in the slightest and does not punish anyone except for a sin that he committed. He is always bestowing His grace upon man, therefore every punishment from him arises from pure justice, and every favour from him arises from His benevolence.