Mark Hughes' side secured two wins from three games in their tour of the United States and will now return to England to face Wrexham on August 4
American midfielder Shea was key to Stoke's flying start at the Union's PPL Park as he started the move that led to Kightly's early goal, before scoring the game's second with a smart finish in the 18th minute.
While Shea was subbed off just after the half-hour mark due to a rash challenge from Philadelphia's Matt Kassel, the 23-year-old former FC Dallas man had already made a fairly significant case to start Stoke's opening Premier League fixture away to Liverpool on August 17.
With Tuesday's match having barely moved out of first gear, Shea set up the visitors' opening goal in the fourth minute, picking up the ball in the centre circle and driving forward before sending a pass to the left-hand side where Marc Muniesa crossed to Kightly, who volleyed home.
The same trio of Stoke players linked up for their second goal 14 minutes later with Muniesa feeding Kightly on the left, who cut in and curled a cross to Shea for a tap-in in the six-yard box.
The victory on Tuesday brought Stoke's tour of the United States to a close with two wins and a loss against Major League Soccer opposition.
Mark Hughes' team will now head back to England to continue their pre-season preparations with a fixture against Wrexham on August 4.