The Liverpool No.4 was judged to have fouled Leroy Sane inside the area five minutes from the end of a meeting with the reigning champions that was short of genuine chances at either end.
After the game, Van Dijk accepted the referee was right to point to the spot and expressed his relief that the incident did not cost his team – as Riyad Mahrez sent the kick over the crossbar.
“It was a penalty and I said it to the referee afterwards as well,” he told Sky Sports.
“It shouldn’t have happened but obviously I’m happy that we didn’t concede.