✅ Answer: This phrase means: 'O Allah, accept the intercession of Muhammad (peace be upon him) on behalf of his followers, and elevate his status.'

However, according to the two following narrations, this phrase, which is not part of the obligatory tashahhud, is not exclusive to the tashahhud of the second rak'ah and can be recited in all tashahhuds.

Please pay attention to the following two narrations:

مُحَمَّدُ بْنُ الْحَسَنِ بِإِسْنَادِهِ عَنِ الْحُسَیْنِ بْنِ سَعِیدٍ عَنْ صَفْوَانَ عَنْ عَبْدِ اللَّهِ بْنِ بُکَیْرٍ عَنْ عَبْدِ الْمَلِکِ بْنِ عَمْرٍو الْأَحْوَلِ عَنْ أَبِی عَبْدِ اللَّهِ قَالَ التَّشَهُّدُ فِی الرَّکْعَتَیْنِ الْأَوَّلَتَیْنِ الْحَمْدُ لِلَّهِ أَشْهَدُ أَنْ لَا إِلَهَ إِلَّا اللَّهُ وَحْدَهُ لَا شَرِیکَ لَهُ وَ أَشْهَدُ أَنَّ مُحَمَّداً عَبْدُهُ وَ رَسُولُهُ اللَّهُمَّ صَلِّ عَلَی مُحَمَّدٍ وَ آلِ مُحَمَّدٍ وَ تَقَبَّلْ شَفَاعَتَهُ وَ ارْفَعْ دَرَجَتَهُ

📚 Tehzib, Vol. 2, p. 92

Translation: Imam Sadiq (peace be upon him) said: The tashahhud in the first two rak'ahs is as follows:

الْحَمْدُ لِلَّهِ أَشْهَدُ أَنْ لَا إِلَهَ إِلَّا اللَّهُ وَحْدَهُ لَا شَرِیکَ لَهُ وَ أَشْهَدُ أَنَّ مُحَمَّداً عَبْدُهُ وَ رَسُولُهُ اللَّهُمَّ صَلِّ عَلَی مُحَمَّدٍ وَ آلِ مُحَمَّدٍ وَ تَقَبَّلْ شَفَاعَتَهُ وَ ارْفَعْ دَرَجَتَهُ

In the following narration, the Imam permits the recitation of the above tashahhud in the fourth rak'ah as well:

بِإِسْنَادِهِ عَنْ أَحْمَدَ بْنِ مُحَمَّدٍ عَنْ أَحْمَدَ بْنِ مُحَمَّدِ بْنِ أَبِی نَصْرٍ قَالَ قُلْتُ لِأَبِی الْحَسَنِ ع جُعِلْتُ فِدَاکَ التَّشَهُّدُ الَّذِی فِی الثَّانِیَةِ یُجْزِی أَنْ أَقُولَ فِی الرَّابِعَةِ قَالَ نَعَمْ

📚 Tehzib, Vol. 2, p. 101

Translation: Bazanti said: I asked Imam Kazim (peace be upon him), 'May I be your sacrifice, is it sufficient to say the tashahhud of the second rak'ah in the fourth rak'ah?' The Imam replied: 'Yes.'

Based on these two narrations, the phrase ' وَ تَقَبَّلْ شَفَاعَتَهُ وَ ارْفَعْ دَرَجَتَهُ' can be said in both the tashahhud of the second and fourth rak'ah, and it is not exclusive to the second rak'ah.