Q Can I make a transaction with 2049 KB?
Depends. If its a block weight of less than 4,000,000 units, then it is possible. The block itself has its own coinbase transaction and that does take up some space. If the size of transaction is 2,049KB and its not segwit, it would most definitely not be accepted.
Q Will it ever get a confirmation?
If a miner is willing to include it, then yes. The problem is likely with that transaction size being too high such that it becomes a non standard transaction and you would have to find a miner to include it specifically.
Q If it will then it will be violation of rule, that a block can't be greater than 2 MB?
No.
There wasn't anything about blocks being limited to 2MB in the first place.
The only thing is that the practical max for Segwit blocks is about 2MB (blocks with all the segwit transactions), IIRC. The maximum size would in theory, be 4MB but 2MB would be about what we can achieve in real life scenarios.
Since the release of Bitcoin Core 0.13.0, the calculation for a max block size is switched to the weight concept instead of a "size" concept. This makes it compatible with the previous versions of Bitcoin Core since it does not violate their 1MB rule as they only see the base data and not the Segwit witness data. There is no restriction with the block size, only block weight.
Q If I'm able to make a transaction with 2049 KB then will it able to clog the bitcoin network or able to make the fees higher to any extend?
No. If you were to make such a transaction, you would have to entice the miner with an incredibly high fee and that effect is only there for only a block. Furthermore, since its non standard, users probably won't even know your transaction exists till it gets mined.