First, know that there aren't any flights straight to South Padre Island. This confuses many people who try plan last minute flights to South Padre Island. The closest airport is Brownsville/South Padre Island International Airport at 20 miles away. (Car, taxi, or hotel shuttle will get you the rest of the way.) If you're having problems finding flights through here, you may have to consider alternate airports.
That said, head to Priceline.com's particular page for last minute deals. They typically contain a combination of airfare and hotel room from providers looking to fill their airplanes and hotels at the last minute. Simply choose your destination of South Padre Island, where you're leaving from, and your travel dates. Priceline scours the Internet for the South Padre Island travel deals that best meet your criteria.