The former Mirror editor hailed a 2-minute rejoinder that opened Thursday night's 'This Week' as "television at its best", after Neil denounced those behind events in Paris as "Islamist scumbags".
"This was one of the great passionate moments that I’ve seen about any of these incidents in a very long time… and coming from a BBC presenter it was incredibly refreshing," he told BBC Radio 2 on Friday.
Morgan lauded the rant, saying it was a "gutsy" editorial move but one that ultimately paid off.
He recounted switching over to BBC 1's Neil-fronted current affairs show after 'Question Time', which saw panelists including Mehdi Hasan and Anna Soubry clash over strategies to respond to the latest terror attack to grip Europe.
"Just occasionally, particularly after watching Question Time last night, which was a sort of to-and-fro between lots of different opinions and voices, and I was watching this...
"And I was thinking about Paris, thinking about the week, thinking about the horror that had unfurled on people, thinking about the fact my wife was born and raised there - I go there all the time - like many of us I’ve walked those streets, and feeling a rising sense of fury as I watched Question Time.
"And then to turn to Andrew Neil immediately afterwards and to have him basically exploding in exactly the way I was feeling was fantastic and television at its best."
He continued: "I really salute him because it was a gutsy thing to do, and it was something I’m sure lots of people would take issue with and say ‘that’s not your place to do that’.
"But I wonder how many people in this country were watching live and feeling like I was -- that this was something you wanted to stand up and cheer it from the rooftop."
Hear Morgan's full comments below
Neil opened his weekly news show yesterday with an unprecedented delivery hitting out as Isis fighters.
“I can’t say I fancy their chances,” mocked Neil, before listing the cornerstones of French civilization, from Monet to Descartes, Rousseau to Camus, Berlioz to Satie, Daft Punk to Zizou Zidane… “Liberté, égalité, fraternité and crème Brulee.”
“Versus what?” he asked. “Beheadings, crucifixions, amputations, slavery, mass murder, medieval squalor and a death cult barbarity that would shame the Middle Ages.”
“I think the outcome is pretty clear to everyone but you,” he surmised.
“You will lose. In a thousand year’s time, Paris, that glorious city of lights, will still be shining bright as will every other city like it. And you will be as dust, along with the ragbag of fascist Nazis and Stalinists that previously dared to challenge democracy and failed.”