Matt McClure put Wycombe in charge after 22 minutes when he turned on to Stuart Lewis' cross and slipped home a low shot.
The home side's woes deepened when defender Danny East was carried off after 37 minutes when he appeared to land on his neck following a fairly innocuous challenge near the centre circle.
Substitute David Connolly earned Pompey a golden opportunity to hit back after 70 minutes when Sam Wood felled him in the box and referee Darren Drysdale pointed to the penalty spot.
Connolly's kick was well saved by Matt Ingram, diving to his right, before Ryan Bird's follow-up was diverted over the crossbar.
But Andy Barcham quickly made up for Portsmouth's disappointment when he lashed a stunning strike high beyond Ingram to level the game after 72 minutes.
Ricky Holmes' free-kick from the right then found Patrick Agyemang, who headed home after 84 minutes.
But Stewart's close-range header in the fourth minute of stoppage time rescued Wanderers a point.