Malaysia's foreign ministry and the Games organisers apologised profusely for the gaffe but it was not enough to quell a wave of complaints online, with #ShameOnYouMalaysia becoming Indonesia's top trending topic on Twitter.
The affected websites display a message in red and white - Indonesia's flag colours - which says: "My national flag is not a toy!"
Indonesia appears to have taken particular offense because the guidebook was distributed to VIPs at Saturday's opening ceremony in Kuala Lumpur for the 29th Southeast Asian Games and only its flag was shown incorrectly.
On Twitter, Indonesians said their flag represents the sacrifices of independence heroes and accused Malaysia of either being stupid or deliberately misprinting it.
President Joko "Jokowi" Widodo demanded an apology for hurt national pride but also cautioned against exaggerating the incident with his neighbor.
Malaysian Youth and Sports Minister Khairy Jamaluddin met his Indonesian counterpart Imam Nahrawi to personally apologize.
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In fact, even those who have already bought their eclipse glasses are still warned to check if they are safe and certified. In the 54 years since that eclipse, he said the blind spot hasn't gotten any worse or any better.
Indonesia's Olympic committee chief Erick Thohir earlier criticised Malaysia's "negligence".
Internet regulators CyberSecurity Malaysia has yet to issue a comment on the matter, but Malaysia's Computer Emergency Response Team (MyCert) released an advisory for administrators on steps to beef up security of their websites.
"However, we ask that no more problems like this happen in the future".
"In this regard, we wish to assure the Government of the Republic of Indonesia that all measures have been taken to address this unfortunate situation.".
It was not the only incident, as another SEA Games booklet mixed up the flags of Indonesia and Thailand in a reprint of the medals table from 2011.
Southeast Asia Games host Malaysia has found itself in hot water after an apparent design flaw in the Games' official booklet drew criticism from Indonesian netizens and government officials.