Because, first, MS Sasuke wasn't a fodder but a main character. Basically Sasuke was a genius and the reincarnation of Indra...
'Then Danzo was old, he was 71 years old. He didn't have a good stamina.
Furthermore, Danzo wasn't at 100% against Sasuke. All he did, was to spare with Sasuke until he recovers his Koto Amatsukami. Danzo's main target was Obito, he saved as much time as possible to use Koto Amatsukami against Obito.
And finally, the plot was against Danzo. He faced a main character, Sasuke needed his revenge, he had to die because of the plot. If there wasn't the plot, Danzo would have killed Sasuke in my opinion, yes if he had used his Izanagi in a wiser way and not stupidly wasted them.
Back in the time, Prime Danzo was an High level Shinobi of Konoha. Not stronger than the Sannin or Hiruzen, but enough powerful to be ranked S. He was in the elite squad of the 2nd Hokage during the 1st Ninja war, and it's not for nothing. Same thing with the fact he had his own Anbu division.