According to the Blues boss, there are no reasons behind his surprise decision to elevate Alex Bass above the Scot in his side.
Instead, Jackett believes the time is right to freshen up his goalkeeping position.
MacGillivray has been left shocked at his axing following 82 appearances as undisputed first choice at Fratton Park.
It is understood the situation has not been driven by rumoured transfer interest, with Rangers previously linked with a move.
While Pompey’s manager is adamant MacGillivray has done nothing wrong.
Jackett told The News: ‘Craig has been number one from day one, for a year-and-a-half, and has just lost his place for two or three games, that’s all.
‘I don't necessarily see a weakness, there wasn’t one incident or one game or a particular part of his game which has led to him being out of the team.
‘Alex has kept improving and I did feel it was the right thing to do. It was a gut feeling.
‘It is not necessarily about kicking, either. Alex, at Gillingham, hit a couple out, there were a couple he mis-hit a little against AFC Wimbledon in the second half as well, but he’s usually a good kicker.
‘Craig has been very, very safe and reliable in that area as well, so I can’t say he (Bass) has something over him in one particular area.
‘Like every player, Craig wants to be in the team, but I can’t say to him “You have to improve on X, Y or Z”.
‘He has asked is there one particular part of his game or one game or one incident, which there isn’t, it’s an overall feeling.
‘You do go with a gut feeling sometimes and it doesn't do anybody any harm to be out for a small amount of time.
‘Craig’s had a great run, I’m sure he will be back.’
Bass is expected to retain his place against Bolton on Saturday, with MacGillivray again on the bench.
Jackett added: ‘I’m confident in both of the keepers, whoever I chose I will have to leave one of them out
‘I will review it game by game.’