Wilkinson discarded the ball in the 47th minute after spotting it was not one of the six marked match balls and informed referee Jonathan Kaplan.
With an official replacement, Wilkinson landed the difficult penalty from near the left touch-line which pulled England to within a point of France at 9-8.
Wilkinson went on to seal England's victory, and a place in the World Cup final, with a penalty and a drop goal in the last six minutes of the game.
The concern for England is that last night was not the first time a non-match ball has made it onto the field.
Wilkinson had been on the lookout for rogue balls after it emerged he had attempted a kick in last weekend's quarter-final win over Australia with a practice ball.
England's director of elite rugby Rob Andrew insisted there was no suggestion of skulduggery - but it is not a situation they want repeated in Saturday's final.
Andrew explained: "A non-match ball got onto the field last night for one of the kicks, which is why Jonny rejected it.
"We didn't say it last week but a non-match ball got onto the field in Marseille, which Jonny kicked and wasn't happy with.
"He didn't stop to think at the time. We noticed it on the video. There were two panels on the same side of the ball, which is not the way the match balls are set up.
"Afterwards we said: 'We have to get this right'.
"The match balls are marked one to six and last night they had 'Semi-final, England v France' and the date on them.
"Jonny was vigilant to ensure they were actually match balls that he was being presented to kick with. We will make sure we have the same vigilance this week."
The issue of match balls was a constant theme in the build-up to the semi-final after England complained they had been over-inflated during the tournament.
World Cup organisers agreed to a change in policy and allowed England and France to practice with the match balls in the build-up to the game - as is common practice for a home Test match - to ensure they were properly "kicked in".