Jakovlevitch is not so much astounded by the fact that he found a nose in a baked roll as he is frightened by the fact that it is a familiar nose, and an official one - belonging to the Collegiate Assessor Kovalev. So, this is a nose with a rank - not high enough to please its owner, but higher than Jakovlevitch's modest social position. Jakovlevitch is afraid: he must have cut off the nose while he was drunk!
Gogol uses the nose to satirize obsessions of Russian society with rank and social status. Kovalev himself is apparently unsatisfied with his status as a civil servant (and that is all he cares about). So, when he sees his nose in a uniform which implies a higher status, he doesn't know what to do, how to behave. He acts as a sycophant. "'How, even so, am I to approach it?' Kovalev reflected. 'Everything about it, uniform, hat, and all, seems to show that it is a State Councilor now. Only the devil knows what is to be done!' He started to cough in the Nose's vicinity, but the Nose did not change its position for a single moment."
He emotionally invested with everything, his emotions overcame him and he could not take it anymore.
