Just over a year ago, the Bush administration pumped $125 billion in new capital into the nine largest U.S. banks in exchange for preferred shares and J.P Morgan Chase (NYSE: JPM) came out a “loser” out of the deal.

At least, that’s the conclusion of two University of Chicago finance professors who say that Morgan Stanley was the big winner of the bailout era, based on which institutions had the most to lose in the absence of unprecedented aid to the banking industry.

Luigi Zingales and Pietro Veronesi have concluded that “Paulson’s Gift,” as they refer to it in memory of the former Treasury Secretary, has added $132 billion in value to the banks. The $132 billion takes into account their debt, common stock and preferred stock. The federal debt guarantees and cash infusions cost taxpayers between $15 billion and $47 billion, according to the two professors in their 49-page paper here.

According to the two professors, the benefits that financial institutions received were very uneven. In their paper, Zingales and Veronesia wrote, “J.P. Morgan shareholders lose $34 billion, Morgan Stanley’s gain $11 billion, while Citigroup and Goldman shareholders gained roughly $8 billion each.”

Other banks included in the original plan included Wells Fargo,Bank of America, State Street Corp and Bank of New York Mellon. Wachovia and Merrily Lynch were also involved in the deal, but they were purchased by Wells Fargo and Bank of America respectively.

“The big beneficiaries of the intervention were the three former investment banks and Citigroup, while the loser was JP Morgan,” concluded the professors.