The results in two mainly rural constituencies were largely expected, as support typically runs strong in such areas for the dominant United Malays National Organisation (UMNO).
The UMNO-led ruling coalition also enjoys huge advantages in money and machinery over a splintered opposition.
0UMNO candidate Budiman Mohamad Zohdi won the parliamentary seat of Sungai Besar of west-central Malaysia, while Mastura Mohamad Yazid won the Kuala Kangsar constituency seat in the country's north, the election commission announced.
The contests -- held after the previous incumbents died together in a helicopter crash in May -- are the first parliamentary electoral contests since the corruption allegations emerged last year.
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But for the second time in as many months, the results provided relief for Najib and his ruling Barisan Nasional (BN) coalition.
Last month, the BN scored a thumping victory in Sarawak state assembly polls to extend its decades-old control of that stronghold state.
"The victory in both the constituencies (on Saturday) will enable Najib to entrench himself as the powerful leader of UMNO," said Oh Ei Sun, a senior fellow at the S. Rajaratnam School of International Studies in Singapore.
It had faced candidates from the Pan-Malaysian Islamic Party (PAS) and Amanah, a new party comprising mostly former PAS members.
Amanah's members split acrimoniously from PAS last year, largely over the latter's increasing Islamic conservatism.
Experts say that likely split the votes of the Muslim ethnic Malays who are the country's majority group.
Najib faces allegations that billions of dollars were plundered from a state-owned investment fund he founded.
The accusations, which burst forth last year, include the revelation Najib received at least $681 million in deposits to his personal bank accounts in 2013.