Tony Adams' side need to win to stay in the competition but Edin Dzeko put the hosts one up on three minutes from close range, although Jermain Defoe equalised on 11 and Arnold Mvuemba's deflected shot put Pompey in front on 14.
Christian Gentner's cross-shot caught David James on the hop to put Wolfsburg level on 23, and the England goalkeeper will also be questioned about the German side's winner on 70 minutes when Zvjezdan Misimovic slotted into an empty net – although James did save the Bosnian playmaker's late penalty.
Meanwhile, Aston Villa surprisingly lost at home to Slovak side MSK Zilina but still went through to the last 32 thanks to Hamburg's win over Slavia Prague. The Villans went two down early on to efforts from Vladimir Leitner and Peter Styvar.
Although Villa could only manage a single goal in response, it was a cracker from youngster Nathan Delfouneso. The 17-year-old Brummie, who has come up through the Villa ranks, bagged a superb left-foot volley on his full debut.
And Hamburg's 2-0 win guaranteed Martin O'Neill's side a top-three finish in the group, sending them through to the knock-outs – unlike poor Pompey.
