Translated from Ustadz Firanda Andirja's Indonesian commentary (Bekal Islam). Quoted verses, hadith and duas keep their Arabic; where the commentary gave its own Indonesian rendering of them, that rendering is not translated and is marked [translation not shown].
(اَللَّهُمَّ عَافِنِيْ فِيْ بَدَنِيْ) that is, asking Allah to keep the body safe from illness and harm, so that a person is strong enough to carry out obedience to Allah and to support His religion.
(اَللَّهُمَّ عَافِنِيْ فِيْ سَمْعِيْ، اَللَّهُمَّ عَافِنِيْ فِيْ بَصَرِيْ). Hearing and sight are then mentioned specifically (even though both are part of the body) because both are the means of recognising rational and textual proofs. With the eyes a person can see the greatness of Allah in His creation, and with hearing a person can hear the verses of Allah that Allah has sent down. This dua resembles another dua of the Prophet:
اللَّهُمَّ مَتِّعْنَا بِأَسْمَاعِنَا وَأَبْصَارِنَا وَقُوَّتِنَا
[translation not shown] (Graded hasan by Al-Albani in takhriij Al-Kalim At-Toyyib, no. 226) (see Faidul Qodiir 2/135)
Part of the well-being of hearing and sight is being kept safe from sin, so that hearing is not used to listen to sinful things and sight is not used to look at the things Allah has forbidden.
REFERENCE
Quoted as the source gives it, in Indonesian.
(11)HR. Abu Daud no. 5090, Ahmad dalam Musnadnya no. 20430, al-Bukhari dalam al-Adabul Mufrod no.701, dan dihasankan (hasan lighoirihi) oleh Al-Albani, Syu’aib Al-Arna’uth dan para pentahqiq al-Musnad karena mutabaah dan syawahid.