A total of 116,048 Likud members are eligible to vote in 106 polling stations across Israel, reports The Jerusalem Post newspaper.
Netanyahu is running against Sa'ar, a Likud lawmaker and a former Education Minister, in one of the crucial challenges in his long political career.
Both candidates spent Wednesday in energizing supporters and making logistic preparations to ensure their voters would arrive at the ballots amid unusually stormy weather that hit Israel.
Netanyahu announced that he would convince the White House to acknowledge Israel's sovereignty over the Jordan Valley, part of the Palestinian West Bank seized by Israel in the 1967 Middle East war, Xinhua news agency reported.
"Only I can make it," he said in video footage released on his Facebook page.
Sa'ar on the other hand, pledged to impose Israeli law on the entire settlement West Bank, a controversial move that would practically annex the disputed territory.
Local media reported that internal polls, commissioned by the candidates' headquarters, predict a landslide victory for Netanyahu.
However, harsh weather conditions could deter many voters from arriving at the ballots.
Earlier in December, Saar, 53, announced that he will run against Israel's longest-serving prime minister, Netanyahu, 70.
The embattled leader is facing criminal indictments in three separate corruption scandals, in which he is charged with bribery, fraud, and breach of trust.
He denies any wrongdoing and says the charges are part of "a witch-hunt".
Netanyahu is currently struggling for his political survival, failing to form coalition governments after the last two national elections in Israel.
However, if he wins the primary, he is likely to stay in office at least until March 2, 2020, when the next national elections will be held.
The unprecedented national elections will be the third time Israelis would cast their ballots in less than a year, amid political deadlock that has paralyzed the Israeli political system over the past months.
( With inputs from IANS )