The bloody incursion by some 200 Islamic militants from the southern Philippines was inspired by a self-proclaimed Filipino sultanate's claims of historical dominion over the Malaysian state of Sabah on Borneo island.
The assault, Malaysia's most serious security crisis in years, led to a siege between the militants and the country's armed forces who were sent to root them out.
At least 70 people were killed, mostly militants, over the six-week ordeal.
The nine had initially been handed life sentences last year but prosecutors appealed for a stiffer penalty.
"With this current sentence, I am satisfied," Deputy Public Prosector Wan Shaharuddin Wan Ladin told AFP.
"Hopefully this will deter other alien nations from intruding into Sabah and Malaysia."
He added that technically the nine Filipinos were sentenced to death for "waging war against the King of Malaysia" and jail sentences of 13 to 18 years were handed out for "being a member of a terrorist group."
Government official Raul Dado said Philippine officials in Malaysia are "meeting immediately with embassy lawyers".
A total of 800,000 Filipinos live in Sabah, making up about a quarter of the population of the state, which is just a short boat ride from the southern Philippines.
The crisis at the time embarrassed both the Philippines and Malaysia, shining the spotlight on a porous border and locals' complaints of rampant illegal immigration and lawlessness.
The sentencing comes as Philippine troops continue an offensive to dislodge militants flying the Islamic State group flag who seized the southern city of Marawi more than two weeks ago.
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