Yes, any excess period must be served.
But I must say your CA is so rude. Who extends the articleship for 45 days ?
I mean if the leaves exceed 100 and so, then the CA should extend the articleship.But 45 days excess and he reported that to ICAI.
You must have argued/misbehaved with him all these years. 
You should have asked for his mercy. LOL.
But he should have, by himself, relieved you with no excess leaves.