Can I create a transaction like this ?

[RocketSingh]

Input amount: 0.01 BTC

Output amounts...
i. 0.009899 BTC
ii. 0.000001 BTC

Mining fee: 0.0001 BTC

Will this Tx face any problem in being included in a block as one output is very low ?

[shorena]

Input amount: 0.01 BTC

Output amounts...
i. 0.009899 BTC
ii. 0.000001 BTC

Mining fee: 0.0001 BTC

Will this Tx face any problem in being included in a block as one output is very low ?

Yes, 100 satoshi is below the current dust limit (546 satoshi) and thus you will have a hard time to get that transaction broadcasted to a miner.

[RocketSingh]

Input amount: 0.01 BTC

Output amounts...
i. 0.009899 BTC
ii. 0.000001 BTC

Mining fee: 0.0001 BTC

Will this Tx face any problem in being included in a block as one output is very low ?

Yes, 100 satoshi is below the current dust limit (546 satoshi) and thus you will have a hard time to get that transaction broadcasted to a miner.

So, do u mean, the following will go fine ?

Input amount: 0.01 BTC

Output amounts...
i. 0.0098945 BTC
ii. 0.0000055 BTC

Mining fee: 0.0001 BTC

[shorena]

Input amount: 0.01 BTC

Output amounts...
i. 0.009899 BTC
ii. 0.000001 BTC

Mining fee: 0.0001 BTC

Will this Tx face any problem in being included in a block as one output is very low ?

Yes, 100 satoshi is below the current dust limit (546 satoshi) and thus you will have a hard time to get that transaction broadcasted to a miner.

So, do u mean, the following will go fine ?

Input amount: 0.01 BTC

Output amounts...
i. 0.0098945 BTC
ii. 0.0000055 BTC

Mining fee: 0.0001 BTC

Yes, that should confirm just fine. Its not nice to send someone 550 satoshi as they will have a hard time to spend those coins though. However if they have other larger inputs to spend they can combine the 550 satoshi with e.g. 1 BTC and have no problem. I would consider it spam though, no matter whether I can easily combine it or not.

Maybe you can use something offchain[1] for the transaction like changetip?

[1] as in: via a service, not via an actual transaction on the blockchain

[RocketSingh]

Thank you for the explanation. In fact this 550 satoshi is the commission amount of an application. Its value will vary depending on the input amount. I needed to know the lowest I can allow. I could leave it in the wallet itself, but as hot wallet is not safe, I want to move out the commission amount as well. Hope, I am doing it right...

[Cryddit]

The system at present does its darnedest to NOT create "dust" txOuts. 

Do you realize that when you use a 550-Satoshi fee, you're dooming the recipient to spending fully a third of it on fees just because of the size increment in the transaction that will be required to use it? 

Also, the dust limit may (probably will) rise in the future, so if you bake a 550-Sat somethingorother into something you're writing, it will break the instant the fee rates change.

[RussianRaibow]

Input amount: 0.01 BTC

Output amounts...
i. 0.009899 BTC
ii. 0.000001 BTC

Mining fee: 0.0001 BTC

Will this Tx face any problem in being included in a block as one output is very low ?

Yes, 100 satoshi is below the current dust limit (546 satoshi) and thus you will have a hard time to get that transaction broadcasted to a miner.

Can you please point me to a source that says 546 satoshi is the dust limit ?

Because, at http://mempool.info/help, I found...

Dust = Transactions with at least one output that is less than 5431 satoshis.

[teukon]

Can you please point me to a source that says 546 satoshi is the dust limit ?

Because, at http://mempool.info/help, I found...

Dust = Transactions with at least one output that is less than 5431 satoshis.

The relevant section of Bitcoin Core's source is here.

Bitcoin Core's default minimum relay fee was lowered tenfold to 1000 satoshis/kB quite some time ago, bringing the dust threshold down with it.  Your source even acknowledges that it is using the "old fee policy of 0.0001 BTC/KB".