Jupp Heynckes's charges set about trying to restore parity but, despite enjoying the lion's share of possession, failed to trouble Wolfsburg's backline and remained a goal down at the break.
The visitors managed to find an equaliser just after the hour mark through Wagner, who headed home from close range following Robben's cross from the right-hand side of the penalty area.
Bayern dominated the latter stages of the encounter and were rewarded with a second penalty in the 90th minute when Gian-Luca Itter brought down Robben, who duly stepped up and rifled into the bottom right-hand corner of the net for all three points.
WOLFSBURG (4-2-3-1): Casteels; Jung (William 78'), Knoche, Bruma, Itter; Guilavogui, Arnold; Steffen (Osimhen), Didavi, Malli (Dimata 90+2'); Origi
BAYERN MUNICH (4-3-3): Ulreich; Rafinha, Martinez, Sule, Bernat; Tolisso, Rudy, Alcantara (Muller 62'); Robben, Wagner (Lewandowski 79'), Ribery (Alaba 66')