Wow, I got really lucky.
I found Suicune like 5 times in the last hour.
So I used my Wobbafett first so I could try to Counter or Mirror Coat it and lower its hit points, but it kept killing me in one hit with critical hits

I always sent out the strongest PKM in my party at the time and then threw an Ultra Ball. It didn't shake at all and broke free right away.
So on my fifth try, instead of sending out my strongest after Wobbafett was defeated, I sent out my weakest; a Lvl 9 Male Nidoran (my HM slave). I threw an Ultra Ball and caught it first try.
So I guess this problem is now solved.