Jonathan won last fall's election by only nine votes and candidate Sheldon Wuttunee appealed.
Jonathan was reinstated to her position in late April by the FSIN's executive council despite calibration errors that were found with a vote counting machine.
That decision went against what an independent appeals tribunal proposed when it found the chief electoral officer was in a conflict of interest that interfered with the democratic process of the election.
The FSIN executive council once again went against the appeals tribunal at the assembly Wednesday, voting to disagree with the tribunal's decision to declare last fall's first vice chief election results null and void.
In all, 43 chiefs voted to support Jonathan, two were opposed and five abstained.
Chiefs from across the province spoke about how important it was for women to play a leadership role in the FSIN and how it provides a voice for First Nations women in the organization.