It turned out that a television viewer had spotted something that had happened on the 17th hole during the third round.
The sanction related to an incident nearly 24 hours earlier, in which she incorrectly replaced a marked ball, that was missed by course officials but investigated following an email from a television viewer.
Thompson wasn't the only one who thought the penalty was a joke.
Ryu So-yeon clinched her second major title after a drama-filled play-off win over Lexi Thompson at the ANA Inspiration. Thompson said after being informed by a rules official, before making birdies on three of the last six holes to force the play-off.
Fans were undoubtedly behind an emotional Thompson, the 2014 champion penalised after a TV viewer emailed the LPGA. "First off I do want to say what I had done was 100 per cent not intentional at all", Thompson wrote on Instagram.
"It's unfortunate what happened", Thompson said. The American could have won it on the 18th green but missed a mid-length putt for eagle.
Thompson fell to 14 under and eventually lost in a playoff to So Yeon Ryu. "Lexi and I had a great match going there. I did not mean it at all", Thompson said greenside.
Rules officials reviewed the film for two hours before alerting Thompson of the violation of Rule 20-3.
Thompson was fighting back tears on the No. 13 tee box when she hit a drive that landed in the left rough.
"I had to regroup myself. Let's go [Thompson], win this thing anyway", Tiger Woods tweeted shortly after the penalty was announced. Every day is a learning process, and I wasn't expecting what happened today but it is what it is. On top of that, consequently, another 2-stroke penalty was tacked on for signing an incorrect scorecard after her Saturday round for not accounting for the assessed 2-stroke penalty.
As awkward as the situation was, it could have been worse: If golf officials hadn't made a rule change a year ago, Thompson would have been disqualified entirely. As a result, her three-shot lead was wiped out by a four-shot penalty. "That's all I can think about right now".
Thompson released a statement on her Instagram following the controversy explaining she wasn't aware of her error, and thanking fans for their fervent support in what was obviously a hard moment. "I learnt a lot about myself, and how much fight I have in me".