They were former Rural and Regional Development minister Datuk Seri Shafie Apdal (pix) and former Natural Resources and Environment minister Datuk Seri G. Palanivel.
Palanivel is Cameron Highlands MP while Shafie is Semporna MP.
Pagoh MP Tan Sri Muhyiddin Yassin, who was dropped as deputy prime minister in the reshuffle, was however, present during the voting.
Opposition MPs had called for a bloc voting, which ended up with 128 votes for the Budget to proceed to the next stage and 74 voted against.
Prime Minister Datuk Seri Najib Tun Razak was also present in the Dewan Rakyat briefly to witness the Budget being voted for second reading.
The next is the committee and final stage of debates for the Budget to be approved.
Seven of the PAS MPs abstained from voting on the Budget, in line with the party's pledge to remain neutral.
PAS parliamentary whip and Pokok Sena MP Datuk Mahfuz Omar was among three MPs from the Islamist party who voted down the Budget.
The two others were Kubang Kerian MP Ahmad Baihaki and Pasir Puteh MP Dr Nik Mazian Nik Mohamad.
It is learnt that independent candidate Tan Sri Abdul Khalid Ibrahim, a former PKR member, threw his support for the Budget.
DAP’s Lim Kit Siang did not vote as he was suspended for six months. Budget 2016 was tabled by Najib on Oct 23.