The two cricketers weren't part of the squad announced on Thursday to tour New Zealand.
Misbah said he and his team are looking to "invest, develop and focus" on young talent that serves the national side across formats.
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Malik, 38, already retired from Tests and ODIs, has been playing T20 cricket for Pakistan and in leagues around the world. But it seems, in wake of a dip in form coinciding with the emergence of some fine young talent, selectors have begun looking past Malik.
Amir's case is slightly complicated and controversial. After his premature retirement from Tests, disappointed authorities also dropped him from T20I set-up last winter.
And although Amir returned as part of an extended squad mandated amid COVID-19 pandemic for the tour of UK in September - a series which he had earlier decided he won't travel for due to the birth of his child - his poor form in the first two games saw him dropped from the playing XI for the third T20I and now, the squad.
"Shoaib Malik and Mohammad Amir are not part of the white-ball matches as for this tour we have opted to invest, develop and focus on the promising and emerging players who are likely to be available to Pakistan for all formats," Misbah said in a media release issued on Thursday (November 11) by Pakistan Cricket Board.
There was also one major exclusion from the Test squad that was announced by Misbah and his selection panel, as they've left out middle-order batsman Asad Shafiq. Shafiq has been dropped due to a prolonged drought of runs, including the tour of England where he managed just 67 runs in three Tests.
"Asad Shafiq has been left out due to lack of form after he managed 510 runs in his last 15 innings, including a total of 67 runs in England," said Misbah.
"Asad is an experienced batsman and I am sure he will utilise this time to work harder on his game in the domestic first-class matches so that he, like Sarfaraz Ahmed, can reclaim his form and be back in contention for the upcoming Tests against South Africa and Zimbabwe."
Pakistan will play 3 T20Is and 2 Test matches on their tour to New Zealand, starting December 18.