Pompey have been fined the maximum £15,000 for failing to comply with the Checkatrade Trophy rules.
The English Football League confirmed 12 clubs have been punished.
Only Pompey and Luton Town have been fined the maximum amount, after breaching the rules in each of their three competition fixtures.
Under the full strength policy, five of the starting line-up must have started the previous or following game, or five of the starting 11 must be players who have made the most starting appearances during the current season.
Pompey have been knocked out of this year’s competition, having lost to Yeovil, drawn with Reading Under-23s and beaten Bristol Rovers.