Ancients don't give a full level?

It's not 1 level of experience, it's "a lot of experience up to 1 level".

From quest info on Diablo 2 wiki:

Reward: Bonus to your Experience. Normal: 1.4 million, Clvl 20 required. Nightmare: 20 million, Clvl 40 required. Hell: 40 million, Clvl 60 required. This bonus is not cut like experience from monster kills when you are past Clvl 75, so this quest is always a huge boost, but if you can save it (borrow a portal to the Worldstone Keep) until you are Clvl 80 or 85 it's even more valuable.

From quest info on Arreat Summit:

Reward: The maximum experience gain is limited to 1 character level.

Also, experience needed to next level on 89 is 134,011,418 (source). You got about 33% on 89 lvl on Hell difficulty, which is ~40kk and matches wiki info.