The 47-year-old awarded Burton a free-kick after ruling Dwight Gayle had encroached beyond the 18-yard line before Matt Ritchie's successful spot-kick.
Football League rules state that a penalty kick should be retaken if the attacking team are ruled to have encroached into the area - but Shroud failed to order the spot kick to be retaken.
Newcastle United defender Chancel Mbemba has posted on Twitter, after making his long awaited return to Rafael Benitez's starting line-up against Burton Albion last night. "Keith and his team and understandably upset at the lapse in concentration and apologise for the mistake", read a PGMOL statement.
On a freaky night at St James' Park, Ritchie struck the victor in the 68th minute to secure the win that keeps Newcastle 10 points clear of third-placed Huddersfield and one ahead of title rivals Brighton.
However, after Ritchie had successfully converted the penalty, the official promptly disallowed the goal before giving a free-kick to Burton, a decision which left the Magpies flummoxed.
Matt Ritchie's victor fired Newcastle top of the Championship again. That would've been the correct call had Ritchie missed his penalty, but he didn't. There was work rate, a lot of positives and unfortunately we talk about the incident.
"We are as critical as anybody at times but once they come out and say, "yes, we made the mistake", that's it, you move on".
Somebody has put the ball in the top corner.
"Hopefully we can get the three points at home and give ourselves a really good chance of staying in this division".
Newcastle are expected to make just one change to their starting line-up which takes on Burton in the Championship on Wednesday evening.