First and foremost: Vyndktvx stole three 'sublime weapons' from Zrfff's vault/arsenal. One of which(the Million-Pointed Multispear) was capable of perma-killing 5-D beings with a single strike... A fact he demonstrated on the Imp King:
http://i.imgur.com/IWgjfUn.jpg
http://i.imgur.com/EwkAYQ2.jpg
*The Multispear also destroyed 230 worlds instantly as a side effect of that one strike. Not sure if MoD can withstand an attack from a weapon that can kill 5D beings. /shrug
Aside from that, Vyndktvx was able to manifest his essence as metatextual thought-form technology *enter "Super-Doomsday"*
"I'm an unstoppable killer franchise from a parallel reality! A thought that gets bigger and bigger the more you think it.":
http://i.imgur.com/SdD7Ikm.jpg
"I'm the thought of a bigger Superman [...] I'm powered by a simple corporate directive: annihilate the competition!":
http://i.imgur.com/QbqJ0lT.jpg
He was also attacking Superman at all points in his timeline simultaneously:
http://i.imgur.com/p9odMa2.jpg
In fact, his battle with Superman was taking place in "A HIGHER-UP world too... In ALL the different worlds there are, ALL at the same time.":
http://i.imgur.com/739znxy.jpg
IOW, the battle was simultaneously taking place across the entire multiverse AND the higher-dimensional planes as well.
Superman ultimately stopped Vyndktvx with a metatextual plot-device just before he destroyed creation:
http://i.imgur.com/THmLtX6.jpg
http://i.imgur.com/ghp0KHZ.jpg
http://i.imgur.com/3EU9wvd.jpg
http://i.imgur.com/2y4OkES.jpg
http://i.imgur.com/9G0fMQG.jpg
