The game, which kicks off tomorrow night at the Volkswagen Arena in Germany, has not been picked as one of the live games, with Five screening Aston Villa's match with MSK Zilina instead.
The channel cannot screen both games because they kick off at the same time.
Uefa regulations state that for the last two matches in the group stage of the competition all teams from each group must kick off at the same time in order to prevent other teams finding out the other results. If they did then it could affect how they play.
The kick-off times are either 7.45pm or 5.30pm.
All the teams in Aston Villa's group chose to kick off at 7.45pm, and Wolfsburg and Portsmouth agreed to kick off in the same slot after Heerenveen and Braga, the other teams from their group, said they preferred it.
Part of the attraction of the Villa game for Five was that it was at home, which makes production easier.
Gary Double, a spokesman for Five, said: 'We had already secured live coverage of Aston Villa's match shortly after the group stage draw.
'The games kick off at the same time so we couldn't show both.'
Mr Double, who in a separate role also acts as a spokesman for Pompey, added: 'If the match had been scheduled for earlier it's something we would have looked at, especially having shown Portsmouth live three times already this season.'
The situation is a second disappointment for fans after the screening of the Uefa Cup game with Braga was also not screened live.
Nigel Tressider, chairman of the Portsmouth Supporters Club, said that the rules on kick-off times need to be changed.
He said: 'I don't agree with the rule that they all have to play at the same time.'
He added: 'There are lots of people who aren't going.Those fans that can't afford it must have thought they could watch it on TV.
'This is a very important game, because if we win we have a good chance of going through to the next round.'
And Tony Goodall, from the Pompey Independent Supporters' Association, said: 'There's massive interest in this game after the Milan game last Thursday.
'There will be a number of people interested to see how Pompey get on. It's really disappointing for the fans.'
A spokesman for Uefa, European football's governing body, said Portsmouth could have asked to play at 5.30pm to avoid the clash with Villa.
He added: 'The draw was in September and the club had until mid-October to arrange a change in kick-off time.
'There's no plans to change the rules because the kick-off times were already given to the clubs well in advance.'
For the Uefa regulations, click
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