Pompey had four players booked and Redknapp admitted he was frustrated by the night's proceedings - especially with the antics of the opposition and the officials.
He said: "I got frustrated with the whole game to be honest. Right from the start I thought the referee had no idea whatsoever.
"It's frightening, they were diving all over the place and nearly every decision seemed to be a booking."
He also booked Braga goalscorer Wason Renteria for trying to persuade the official to caution Pompey substitute Nadir Belhadj for a foul.
But Braga coach Jorge Jesus said: "Our players only went down because of the Portsmouth players' fouls. We thought the referee did a good job."
Redknapp added: "A few weeks ago we had a great Turkish referee in Guimaraes near here and it was a good game. This time I thought it was very poor.
"They (Braga) played well and deserved to win the game but some of the things they were doing were not right.
"It doesn't happen in our game in England.
"Where is the referee from? Slovenia? I'm sure they have a big league there and plenty of top matches.
"But we didn't pass the ball well and never got going. Our final ball was poor, although I thought we had a perfectly good goal disallowed. At 2-1 it could still have changed the game but I don't know why it was disallowed after seeing it again.
"We missed Glen Johnson who has a pelvic injury and Lassana Diarra who has a bad knee. We never looked at our best.
"But we are still in with a chance of qualifying for the next round. We've got two big home games in the group, one against AC Milan, and there's still all to play for."
Uruguayan Luis Aguiar fired a fabulous 30-yard free-kick past David James in the eighth minute and Colombian Renteria added a second just after half-time.
Portsmouth conceded a third three minutes from time when Sean Davis steered a right-wing cross against his own post and Brazilian Alan pounced to score from the rebound.