Ndlovu netted his second goal of the campaign as he gave his side an early lead after a one-on-one chance with the keeper, which they then doubled through Eyal Golasa.
But PAOK, who last year had South African Bongani Khumalo in their side, stormed back to win the game 3-2, and could even afford to miss two first half penalties, with Ndlovu replaced at half-time.
Haifa’s chances of reaching the second round now look distant as they have just a single point from their opening three games.
There was also some frustration for Anele Ngcongca’s Genk as they let a late lead slip at home to Rapid Vienna to draw 1-1.
They still head their pool though and look a good bet for the next round.
Staying in Group G, South African-born Lukas Schenkel played for Swiss side FC Thun as they went down 3-0 at Dinamo Kiev. That result has seen them drop out of the top two in the pool.