The perfectly judged header from Lewandowski was his 50th goal of the season, and 35th in the Bundesliga for the campaign, and it followed an opener from Josip Stanisic.
At 2-0 in front after 40 minutes, Bayern looked to be cruising, but Jonas Wind and Max Kruse surprisingly brought the home side back to level terms.
Lewandowski, who has told Bayern he wants to leave, could not find another goal as Bayern was forced to settle for a point in the final game of Julian Nagelsmann's first season at the helm.
Leon Goretzka was denied by a smart early save from Koen Casteels after Thomas Muller's clever ball over the Wolfsburg defence picked out the midfielder's run, and Bayern was soon in front.
The opener came from Stanisic in the 17th minute as the Croatian defender sent a header looping beyond Casteels from Joshua Kimmich's right-wing corner.
Bayern doubled that lead when Lewandowski nodded Muller's cross from the right flank into the left corner. It was his 35th goal in the Bundesliga this term, and gave Muller an 18th assist, with both tallies being league highs.
Wind pulled one back when his shot on the turn arrowed past Manuel Neuer in the 45th minute, and surprisingly the home side drew level in the 58th minute as Kruse stretched at the far post to tap in a low cross from the left from Micky van de Ven.
Lewandowski saw a powerful strike well held by Casteels, Serge Gnabry had a menacing shot deflect just over for a corner, and Kimmich almost scored directly from that set-piece.
Bayern was unbeaten in its previous 13 Bundesliga matches against Wolfsburg (won 12, drawn 1, lost 0), outscoring its opponent 46-8 during that run, so the fightback here was a jolt to the champion's system.
Eric Choupo-Moting fired just wide before Leroy Sane missed a glorious late chance to give Bayern a winning finish to the season, running through on goal before dragging a left-footed shot wide of the right post.