After seeing his side beaten by Borussia Dortmund in the German season-opener for the past two years, the Catalan head coach finally looked set to lift the trophy at the third attempt thanks to Arjen Robben's strike just after half-time.
However, Nicklas Bendtner forced penalties with an 89th-minute equaliser before then converting the decisive spot-kick to earn Wolfsburg a 5-4 shootout success - and a first ever DFL-Supercup triumph.
Despite going so close to victory, questions were once again asked about Bayern's mental strength and defensive solidity under Guardiola but the former Barcelona boss claimed his troops had been unlucky to lose.
"It's a pity because we just had to defend for about two or three [more] minutes," the 44-year-old told reporters after the game at the Volkswagen Arena. "We haven't played badly.
"It's not easy to play against such a great team, a team that did very well last season and will play in the Champions League this season.
"Wolfsburg play very wide, have a good direct passing game and put in dangerous crosses. Obviously the Bundesliga, DFB-Pokal and Champions League are more important but a trophy is a trophy. It’s a shame. We did well and made chances.
"All of my players battled away and covered lots of ground. We did everything we could to win the match, but congratulations to Wolfsburg, who also did very well.
"We will try to get here again next season by winning the championship. It goes on and on. First, the Audi Cup, then the match in the DFB-Pokal, and then the start of the Bundesliga. We now focus on the next goal."
Bayern kick off the defence of their Bundesliga title with a meeting with Hamburg at the Allianz Arena on August 14.
