Pełczyńska-Nałęcz, the Minister of Funds and Regional Policy, won 350 votes in a re-run of the second round, defeating Climate and Environment Minister Paulina Hennig-Kloska, who received 309.
According to the grouping's press office, 659 party members took part in Saturday's ballot, which began at 4pm and concluded after 10pm.
The initial second-round vote on 12 January was annulled due to technical problems with the online voting system.
The party's National Council decided on 19 January to hold a fresh ballot.
The leadership contest has sparked a crisis within the party.
Outgoing leader Szymon Hołownia, who also serves as speaker of parliament, met both candidates last week, urging them to work together regardless of the outcome.
Proposals to restart the election from scratch – which would have allowed new candidates, including Hołownia himself, to stand – were rejected.
A suggestion that the two candidates serve as co-chairs also failed to gain support.
Poland 2050 holds 31 seats in parliament, making it the third-largest party in the governing coalition.
However, opinion polls suggest it would struggle to cross the electoral threshold in a general election.
(ał)
Source: IAR, PAP