If He made the Takbir for the Sunnah Prayer, then the Prayer began
Question :
A man entered the mosque to perform the Sunnah of Zuhr and after he made the Takbir, the prayer started... Should the man break off his prayer, or complete it? I request an explanation of this matter.
If the prayer begins while one of the congregation is praying Tahiyyatul-Masjid, or the fixed Sunnah prayers, he should break off his prayer and prepare to offer the obligatory prayer, as the Prophet said:
If the (obligatory) prayer begins, then there is no prayer except the obligatory one.
Some scholars held the view that he should complete it quickly, based upon the Words of Allah:
O you who believe! Obey Allah and obey the Messenger and render not vain your deeds.
And they interpreted the above-mentioned Hadith as pertaining to one who began the (Sunnah) prayer after the Iqamah. But the correct view is the first saying, because the aforementioned Hadith covers both situations. Other Hadiths have been narrated which prove that this is general, and that he spoke these words when he saw a man praying while the Mu'aththin was calling the Iqamah. As for the Qur'anic Verse, it is general, while the Hadith is specific. And the specific takes precedence over the general and does not contradict it, as is known from the study of Usulul-Fiqh and Mustalatul- Hadith.However, if the prayer begins and the person has already performed the second Rak'ah, there is no sin in completing it, because the prayer is almost over and nothing remains from it except a small part of one Rak'ah. And Allah is the Granter of success.
Source:
Ibn Baz
Fatawa Islamiyah, Vol. 2 Pages 297-298