"That door is completely shut, Kevin will not be picked. That's from me," Morgan told the Daily Mail.
South African-born Pietersen, a former England captain and member of the side that won the World Twenty20 in 2010, was dropped in 2014.
England director of cricket Andrew Strauss explained the decision at the time by saying there was a "massive trust issue" with Pietersen. The pair had fallen out over text messages sent by Pietersen to South African players during a 2012 test series when Strauss was captaining the team.
Pietersen responded to Morgan's comments on Twitter.
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"Interesting he's saying it's HIS call! Very interesting! Hmmmmm," said Pietersen, who is England's second highest run-scorer in Twenty20 internationals.
Morgan, top of that list, has led a revival in England's one-day fortunes since their dismal first-round exit at last year's 50-over World Cup.
They lead hosts South Africa 2-0 in the current five-match series.
(Reporting by Ed Osmond in London; Editing by Mark Trevelyan)
