Wagner (4-3) retired the first two batters in the ninth before Jose Vizcaino reached on third baseman David Bell's fielding error. Willy Taveras beat out an infield single to shortstop, and Biggio followed with a drive into the left-field seats for his 20th homer.
"I tried to get it up, but that's his zone," Wagner said. "You have to make sure it's up enough."
Making matters worse for Philadelphia's All-Star closer, Biggio just signed a jersey for Wagner's son.
"Here you go, son, here's a jersey from the guy who just homered off your dad," said Wagner, who got the loss for the second straight game after not facing Houston the first nine times the teams met since he was traded to Philadelphia in 2003.