The 24-year-old striker, who initially moved to Latics on loan from Leicester in January before the move was made permanent, started the game on the bench but was called into action in the seventh minute when Marc-Antoine Fortune had to come off due to injury.
On the half-hour mark, he opened the scoring by heading home James Tavernier's cross from the right.
The Turkish visitors soon equalised through left-back Koybasi Ismail's curling free-kick, which eluded the stretching Scott Carson.
However, six minutes after the restart, Waghorn was presented with the chance to restore Wigan's lead from the penalty spot after Atiba Hutchinson brought down Callum McManaman in the area, and he made no mistake.
New £2million striker Oriol Riera played the final half hour during which substitute goalkeeper Ali Al Habsi made several fine saves to thwart Besiktas, who will enter the Champions League at the third qualifying round stage next month.
Uwe Rosler takes his men to face Rochdale at Spotland in their next pre-season assignment on Saturday.