Jurgen Klopp's men came into the clash at Signal Iduna Park with a record of two wins in their last 13 league fixtures, but looked set to claim a rare victory against Wolfsburg until Naldo netted a late winner.
The Brazilian defender punished the home side's poor marking when he rose unchallenged to head the 85th-minute leveller from an inswinging corner.
Ciro Immobile's impressive strike had looked to have handed Dortmund victory, but they were unable to see the game out.
Pierre-Emerick Aubameyang opened the scoring with his first goal in six games in all competitions, before Kevin De Bruyne restored parity with a dipping free-kick.
The single point sees Dortmund end their final home fixture of 2014 in the bottom three, while Wolfsburg are now 11 points behind runaway leaders Bayern Munich.
Klopp next takes his side to basement club Werder Bremen on Saturday likely needing a win to ensure Dortmund do not spend the festive period rooted in the drop zone.
Bremen found themselves on the end of a 4-1 hammering at Borussia Monchengladbach on Wednesday.
Max Kruse fired the home side in front from the penalty spot shortly after the half-hour mark, before Oscar Wendt's chip made it 2-0 at the break.
Zlatko Junuzovic curled in a free-kick to reduce the deficit six minutes into the second half, but Christoph Kramer restored the two-goal advantage with a 64th-minute header.
Luca Caldirola received his marching orders after seeing two yellow cards in three minutes, before Branimir Hirgota put the result beyond doubt with a tap-in.
Bayer Leverkusen kept up the pressure on the top three with a 1-0 win at Hoffenheim, while Schalke also remain in touch thanks to a 2-1 victory at Paderborn.
In the day's remaining fixture, Eintracht Frankfurt and Hertha Berlin shared the spoils in an eight-goal thriller at the Commerzbank-Arena.
Goals from John Anthony Brooks, Anis Ben-Hatira and Julian Schieber sent the hosts into a 3-0 lead, before Stefan Aigner and Haris Seferovic hauled Hertha back into the tie.
Peter Niemeyer appeared to have sealed all three points when he found the net 10 minutes from time, but a last-gasp brace from Alexander Meier ensured Frankfurt salvaged a point.
