Mr Thabane announced he would be stepping down in July because of old age, without commenting about the case.
His current wife Maesaiah Thabane has already been charged with the murder.
He would be the first African leader to be charged with a domestic murder while in office.
Lipolelo, 58, was shot dead two days before Mr Thabane became prime minister in 2017.
At the time, he described her killing as "senseless" but police now accuse him of being involved in her killing.
Lipolelo was gunned down at close range on the side of a dirt road while returning to her home in a small village on the outskirts of the capital, Maseru.
She was involved in bitter divorce proceedings with Mr Thabane when she was killed. But Lipolelo had already won a separate legal battle to be recognised as first lady, as opposed to Maesaiah.
At the time, the prime minister was living with Maesaiah, 42, as if she were his wife.
Maesaiah accompanied Mr Thabane to his inauguration, following his estranged wife's death.
Two months later she and Mr Thabane got married in a Catholic ceremony held at a packed stadium in Maseru.