Arjen Robben's second-half dismissal for two needless bookings - the first a dive on the edge of the area - gave Kovac some unnecessary concern, but James Rodriguez popped up in the 72nd minute to curtail a four-game competitive winless run.
Lewandowski had earlier struck either side of half-time to establish a two-goal buffer that was reduced through Wout Weghorst soon after Robben's departure.
But, a day after Bayern president Uli Hoeness labelled press treatment of the club a "joke", the headlines are kinder for Kovac thanks to Colombia star James, a player with whom he has reportedly shared a tense relationship.
Scoreless in five matches for club and country, Lewandowski's struggles initially continued when his mishit follow-up to a Robben effort allowed Koen Casteels to scramble the ball off the line.
Salvation soon came for the Poland international as, in the 30th minute, he read Thiago Alcantara's dummy of a Mats Hummels pass and finished through the goalkeeper's legs.
Casteels denied James before the break only for Wolfsburg to gift away the second within three minutes of the restart, defender William's backward header presenting Lewandowski with a simple one-on-one finish.
An unlikely lifeline for the hosts came through Robben's second booking for a trip on Elvis Rexhbecaj and they took advantage six minutes later as Yannick Gerhardt squared for Weghorst reduce the deficit.
However, the hope proved to be fleeting, James profiting from a fine Lewandowski pass to get the champions back on track in the Bundesliga.
Performance matches result
Kovac claimed in his pre-match press conference that Bundesliga champions Bayern were performing well despite recent results and his comments were justified at Volkswagen Arena, a dominant first half allied to a resilient last half hour that demonstrated a team in good working order.
