Guimaraes then rubbed salt into the wounds by beating Pompey in the post-match tie-breaker penalty shootout to complete an awful night for Paul Hart's men.
Hart decided to field a young side for what he thought would be 60 minutes of the match although David James played his first pre-season match after recovering from injury.
The hosts may have had the better of the first 20 minutes but couldn't conjure up any notable efforts bar an ambitious 40-yard lob from Milhazes that James had to tip over the bar. Richard Hughes had to be taken off early on with an ankle injury and was replaced by Eugen Bopp.
David Nugent should have given Pompey the lead after lobbing Nilson but he was wrongly adjudged to be offside. Guimaraes then had a goal chalked off, correctly, for offside after a nice backheel to Douglas.
The main talking point of the first half would be the downright awful officiating of the first half as Paris Cowan-Hall was booked for a fairly moderate challenge and yet Milhazes got away with two terrible challenges without even a talking to from the Portuguese referee!
Pompey's stout defending meant the game was goalless heading into the break but things fell apart in the second half after Cowan-Hall tripped Targino who went down in the box like he had been shot.
The Pompey youth received a second yellow card and was inexplicably dismissed but it looked like justice had prevailed when Moreno crashed his spot kick against the post.
Unfortunately the hosts did score after a poor defensive header from Marc Wilson allowed Rui Miguel, one of eight half time substitutes, to find space and pick his spot to score.
Kanu came on for David Nugent for his first pre-season appearance but bar one long range effort from Matt Ritchie, Pompey had no attacking threat.
When Paul Hart tried to introduce more subs, the match officials wouldn't let him as ridiculously the tournament organisers decreed that only three subs were allowed to be made during each half, with unlimited changes allowed to be made during half time, much to Paul Hart's amazement.
The Pompey bench became more frustrated as Guimaraes players were going down very easy in a poor show of gamesmanship, the worst coming from Targino who went down holding his face when the ball had clearly hit his leg.
Guimaraes made sure of the win three minutes from time after Custodio headed in Carlitos' corner. There was a penalty shootout to follow to decide a tie-breaker should two teams be level at the top of the table after the tournament and the hosts won that 3-2 to underline a bad night for Pompey.
There were some positives to take from the match, though. Paris Cowan-Hall looked good once again until he was sent off and Modeste M'Bami did a good job in midfield, doing himself no harm in winning himself a permanent contract.
I was also very impressed with the maturity of the young back four. Joel Ward, Martin Cranie, Marc Wilson and in particular James Hurst all showed that they are all competent defenders with bright futures ahead of them based on this showing.
It's just a real shame that Pompey were beaten by a team that resorted to cheap, dirty fouls that went unpunished by an incompetent referee in a tournament where the guests aren't even made clear of the rules.