Was your general a night fighter? If so, he could attack one stack in isolation without adjacent ones reinforcing. I think it's probably the single most important late game general skill (the one reducing siege times coming a close second) and so I gave it to all the fighting generals I could.
Sabotaging an enemy army can also prevent it reinforcing, but I found this a little more glitchy (sometimes they were sabotaged and yet did reinforce - never figured out why).
You would still suffer attrition in one on one fights and if you did not have a big qualitative advantage, it would be costly. But night fighting can be a way for a single elite force to thrash multiple inferior enemy stacks, as veterans of Rome Total War: Barbarian Invasion can testify.
Perhaps as you did, I found the AI rather passive when faced with a single elite player army - it does not seem to want to try to use its multiple stacks to overwhelm you. So you may have had the time to dismember their horde at your leisure.
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