on economic growth and Second Welfare theorem While I was studying eighth edition of Mankiw's Macroeconomics, in chapter 9 on Economic Growth(pg. 245), the author mentions :

"Some economists have proposed increasing the incentive to save by replacing the current system of income taxation with a system of consumption taxation." 

Here, the book was discussing on the topic of government policies that affect rate of saving and spur growth. My question is that doesn't this finding contradicts with Second Welfare Theorem in Microeconomics, according to which, the taxation should be on endowments and not on consumption goods so that we can have Pareto Efficient allocation(refer Varian's Intermediate Microeconomics eighth edition Ch. 31, pg 605)? Or am I wrong in superimposing the micro concept over macro?
The two statement say two completely different things. So, no, there is no contradiction.

The second welfare theorem essentially says that a system of transfers that results in an efficient allocation can be supported by a competitive outcome. The statement about replacing income taxes with a consumption tax will increase peoples' incentives to save. These are two completely different statements.

Your mistake is that you suppose that the second welfare theorem prescribes a system of taxation to achieve the hypothetical transfers. It doesn't. The second welfare theorem just supposes that these transfers can be made---nothing more. Importantly, the alleged social planner who makes the transfers has complete information about the agents in the model. When information about the agents is hidden from the social planner (information such as the skills and true abilities of each individual), such transfers become difficult and costly. That is, they create distortions. This was a point that was famously made by James Mirrlees in his seminal paper "An Exploration in the Theory of Optimum Income Taxation" (1971). The point of this paper is that there is a trade-off between equity and efficiency. Once we consider the fact that transfers are costly and create distortions, the question is, how do we create a tax system that minimizes the amount of distortions and still is able to make desired transfers of wealth. This serves as a motivation for why people might study the incentives created by an income tax or consumption tax, for example.