I was in the US previously on Feb 28'2007. After completion of the assignment, I returned to India on this date
After which, I returned to USA on another assignment on July 5'2009. I was in India continuously from the duration of March 1 '2007 to July 04 ' 2009.

As per the data points given above, do I qualify as a Bonafide resident of India, which will enable me to file the form 2555-EZ to claim foreign income exclusion. My income (from Indian salary) for the period of Jan 2009-June 2009 is below the $91,000 threshold.

Are you married? If not, you will file dual status tax return for 2009.
You are nonresident up to July 4, 2009 and resident after that since you have completed SPT in 2009. Your U.S. Tax Return: Substantial Presence Test

As MukatA correctly points out, you are dual status in 2009.

Perhaps you are confused by the wording in the 1040NR instructions. In your case, you are an Indian national who worked in India during the first part of 2009. Since personal service income is sourced where the work is performed your Indian income is not exposed to US taxation (even if you worked for an American company and even if your salary was deposited in an American bank). Only your US sourced income from July on is taxable in America.