The Republican governor vetoed the legislation last week on grounds it was too expansive in providing publicly funded healthcare for women but the GOP Legislature overrode the veto, the Christian Science Monitor reported.
The override vote was 36 to 16.
The law gives state-funded prenatal care to low-income, illegal immigrants.
After his veto was overridden, Heineman said he is worried Nebraska could become a "sanctuary" for undocumented immigrants because it is now the only state in the Midwest that provides prenatal care for them.
"Providing preferential treatment to illegals while increasing taxes on legal Nebraska citizens is misguided, misplaced and inappropriate," the governor said in a statement Wednesday.