Argentine Pastrana in particular was heavily criticised over the weekend and SANZAR referees head Lyndon Bray wasted little time in following through on his threat from last week.
Bray had said he would be conducting a purge of referees by the end of March in order to hold match officials more accountable for their performances.
"One of our core strategic objectives is to grow the depth of the team that is able to referee 'any game, any time,'" Bray said in a SANZAR statement.
"In line with this, we have reduced the size of the team heading into the next phase of the competition and in doing so, have recognised who has performed to expectation and who has not.
"The aim is to give this smaller pool of referees more game time so when it comes to the finals series, there's a great deal of pressure around who will earn those highly sought after appointments and ... that the competition is getting a consistent high standard of refereeing."
It is the second successive week that Bray has had to face questions about referees after a series of controversies and blunders in the early stages of the competition.
Last week he posted several video clips of contentious decisions on the organisation's website, explained the rationale behind some of the decisions, and then determined whether they were correct.
Pastrana paid the price for his handling of the Blues' 40-30 victory over South Africa's Cheetahs at Eden Park, where the home team scored 17 unanswered points after flanker Boom Prinsloo was dubiously given a yellow card.
The Argentine also seemed to ignore his television match official's advice in awarding a contentious try to George Moala when Prinsloo was off the field.
The television official had said Moala made a double move in scoring, but the Argentine seemed to misunderstand the advice and awarded the Blues the try.
Pastrana has been replaced by Nick Briant, who will now referee Friday's game between Canterbury Crusaders and Wellington Hurricanes in Christchurch.
South African referee Stuart Berry, however, has escaped being dropped from the now 15-strong panel despite being heavily criticised by visiting coaches for his performances involving South Africa's Lions.
He controversially awarded a try to the Lions in their 39-36 victory over the Auckland Blues last week, a decision that Bray later said had been incorrect.
The Queensland Reds were also incensed at some of Berry's decisions in their 23-20 loss to the Lions in Johannesburg on Saturday, when the home side came back from 20-3 down to win.
Berry issued two yellow cards to Reds players and had a 16-4 penalty count in favour of the Lions.
"I've never seen that in a game before in my life," Reds coach Richard Graham told Australian media on Sunday of the penalty count.
"It would be fair to say that I felt aggrieved at the end of the match when we were down to six forwards and a back on the scrum and we're going forward and (the Lions front row) stand up and we're not rewarded."
- Sports & Recreation