I have save teamsite as site template with custom master page applied to it.However when I create new site from this template, newly created site don't apply the custom master page to this site.
How did you apply your custom master page to your team site? I assume you enabled the Publishing features (both site collection and site level) however saving a site as a Site Template which has publishing features enabled is not supported by MS. You could
potentially create a custom Web Template which is based on a Team site site definition that has your custom master page applied.
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