The visitors took the lead on 11 minutes with a Jake Jones goal. PNE equalised five minutes later from Michael McClellan.
Walsall took the lead for the second time from Joe Butlin on 26 minutes. Michael McClellan scored his and the Lilywhites second with an injury time penalty.
This was the second match in four days after a 4-1 home victory over Wrexham last Saturday. The Dragons had scored first before Luke Clarke equalised. Daviel Devine gave PNE the lead before a brace from Will Hayhurst made it 4-1.
Preston remain in seventh position and have not seen a league defeat since 16 October when Stanley beat PNE 4-2.