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I used a master ball to catch Zekrom but I'm wondering... could I have defeated him and the catch him afterwards like I did in original Black?


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Yes, you could have.

After catching Zekrom or Reshiram (or knocking it out), N will appear and will tell you to return to the Giant Chasm to find another of his 'friends.' He'll...

Dragonspiral Tower, Marriland

If you defeat Zekrom, he will reappear after you defeat the Elite Four.

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I meant like defeating Zekrom and then him still being there and let me catch him without having to fight him
Oh, okay.
No, he won't still be there after you defeat him. He will be gone until you defeat the Elite Four. Then he will reappear and you get to re-battle him then.
Am I missing something?
Nope. You nailed that right on the head