The Flyers ended a two-game skid and moved two points ahead of the idle New York Rangers into first place in the Atlantic Division.
Philadelphia's Scott Hartnell got a wrist shot past Niklas Backstrom to tie the game in the second period and Knuble put the Flyers in front with a power-play goal 5:10 into the third.
Upshall gave the Flyers some insurance seven minutes later.
Backstrom made 18 saves in taking the loss.
The Wild had won their two previous games.