There's no doubt that Dylan's performance of "Masters of War" in Hiroshima, Japan 2/16/94 held special significance. It was the only place out of 14 dates during that Far East tour where the song was performed.

"Masters of War," however, is no simple or general anti-war protest song. Written during the winter of 1962-63 against the backdrop of the height of the Cold War, it is, like most of Dylan's other topical compositions from the period, very much a product of its specific moment in time.
That period in the early 1960s was marked by an odd tension. With the dire challenges of WWII fading in the rear view mirror, America was in the midst of a postwar economic boom which produced one of the most widespread and dramatic increases in economic prosperity the world has seen. The hyper growth in industrial capacity that helped American and its allies win the war against fascism was now being harnessed to a new purpose - brand new consumer products and technologies to advance the average standard of living of much of the populace.
At the same time, there was always in the background, if not the forefront of people's minds, a general awareness among US citizens that we were - at least supposedly - living under the constant, possibly imminent threat of total nuclear annihilation. This fear reached its peak just a few months earlier during the Cuban Missile Crisis, when many people tried to get to sleep one night while wondering if there would be a world to wake up to the next morning.
So although we weren't actively involved in any large-scale armed conflict, war was a topic very much on many people's minds, and that was reflected in many of Dylan's early songs.

Among them, "Masters of War" stands out as the most sophisticated of Dylan's takes. "Blowin' in the Wind" with its question, "How many years must the cannonballs fly?" reflects the wistful idealistic hope for an end to war. "With God on Our Side" examines the faulty premise on which individuals and societies can be motivated to mount wars against their fellow human beings. But "Masters of War" zeroes in on perhaps the most sinister force that can propel countries into wars: the individuals and corporations who view armed conflict as nothing more than an opportunity to reap gigantic profits.
Two years before Dylan wrote it, in January 1961, President Dwight D. Eisenhower in his farewell address had warned American citizens they must guard against "the acquisition of unwarranted influence...by the military-industrial complex."
This undue influence - and the idea that arms manufacturers might try to shape foreign policy just for their own selfish economic benefit - is exactly what Dylan's takes aim at in "Masters of War."
In an interview on September 10, 2001 (note the date!), he specifically noted the connection:

"Masters of War"… is supposed to be a pacifistic song against war. It's not an anti-war song. It's speaking against what Eisenhower was calling a military-industrial complex as he was making his exit from the presidency. That spirit was in the air, and I picked it up."

The song's dour, deadly-serious tone reflects the virtually helpless rage individuals may feel when trying to confront such powerful enemies who are so difficult to touch. The most any single person can do to combat them, Dylan implies, is to unmask them - to state clearly for those who don't see it what their evil game really is.

The grimness of the task, and the almost hopeless wish that somehow these enemies of life and mankind can be defeated, is reflected throughout the lyrics.
But two verses especially encapsulate the feeling for me:

"But I see through your eyes and I see through your brain
Like I see through the water that runs down my drain."

and the gut-shaking finale:

And I hope that you die
And your death’ll come soon
I will follow your casket
In the pale afternoon
And I’ll watch while you’re lowered
Down to your deathbed
And I’ll stand o’er your grave
’Til I’m sure that you’re dead

One image that strikes me so indelibly in this final verse is its description of the warmongers' funeral procession taking place "on a pale afternoon." There's no sense of jubilant triumph over one's foes as in "When the Ship Comes In." Perhaps it reflects the sense of helplessness against such diabolically disguised hidden villains who are capable of such extreme malevolent influence.
But it's a vision of their eventual defeat that one most cling to anyway.