The Zephyrs won the series by taking three of four, and have now won six of the eight meetings with Round Rock this season.
Bonifacio's double came one out after Danny Richar doubled off Express reliever Evan Englebrook. It was the third hit of the night for Bonifacio, who joined the Zephyrs on Friday from the Florida Marlins.
The 11th inning rally made a winner of Scott Strickland (3-0), who pitched two scoreless innings and worked around a leadoff walk in the 10th and a leadoff single in the 11th.
The lack of hitting with runners on base was the theme of the night for Round Rock, who went 2-for-20 with runners in scoring position. The Express stranded 20 baserunners on the night, including leaving the bases loaded in the third, sixth and eighth innings.
The Express also saw manager Marc Bombard and first baseman Chris Shelton ejected from the game as frustrations boiled over.
The Zephyrs scored single runs in the sixth, seventh and eighth innings, with none of them coming on base hits. Bryan Petersen scored on a Roy Corcoran wild pitch in the sixth, Brett Hayes doubled and scored on a Bonifacio ground out in the seventh, and Logan Morrison tripled and scored on a passed ball in the eighth.
Game Notes: The Zephyrs and Express played 11 innings and the time of game was 4:27, longest of the season ... New Orleans improved to 12-4 when playing on Patriots' Day.
Coming Up: The Zephyrs return home on Tuesday to open an eight-game homestand. The Zephyrs will start RH Matt DeSalvo (0-1, 9.82) against Isotopes RH Josh Lindblom (0-0, 7.88). RADIO: 106.1 FM WMTI