Azahari was gunned down by Indonesian police on November 10, along with two other men. Although reports were confused at first, his identity was later confirmed.
The former Universiti Teknologi Malaysia (UTM) lecturer had been on the most wanted list of the region's terrorists for his involvement with Jemaah Islamiah (JI), an Islamic extremist organisation blamed for bombings in Bali in 2002 and 2005, as well as the 2003 devices planted outside the Australian embassy and JW Marriott hotel in Jakarta.
While his demise is seen by analysts as a blow to his brand of extremism and a loss for JI's leadership, the operational impact on the militants of losing Azahari is not expected to be that great. He was known to be a good teacher and to have actively sought to pass his skills on.
The authorities in Indonesia moved quickly to find their next targets, among whom was another Malaysian and former UTM colleague of Azahari, Nordin Mohd Top, who police claimed narrowly escaped an operation in East Java launched simultaneously with the action against Azahari.
Indonesian police have since sent a team to Malaysia to work with local police in a bid to trace Nordin and investigate his activities, particularly with regard to individuals he and Azahari may have recruited.
Malaysian press also reported that Wan Min Wan Mat, another former colleague of Azahari and Nordin, had been taken back into custody recently. He was originally arrested in September 2002 under the Internal Security Act (ISA) after he was alleged to have been the financier of JI's operations, as well as another culprit in the 2002 Bali bombings.
Indeed, the Malaysian government claims Wan Min Wan Mat has been a prominent member of Kumpulan Militan Malaysia (KMM), a terrorist organisation based in northern peninsular Malaysia and linked to JI.
The group's mission is similar to JI's stated goals of establishing an Islamic state covering Malaysia, Indonesia, Brunei, southern Thailand and parts of the Philippines - essentially, the creation of a pan-South-east Asian Islamic state.
However, the actions of KMM within Malaysia were limited from an early stage. Indeed, former Prime Minister Mahathir Mohamad has always claimed that Malaysia began its war on terrorism long before President Bush inspected the rubble of the former World Trade Centre in September 2001; the early moves against KMM are evidence of this.
In the late 1990s, the government moved swiftly to stamp-out nascent terrorist activity, which was at that stage largely domestic. The group was even linked to the opposition Islamic Party of Malaysia (PAS), some of whose members were arrested in the crackdown.
For many, the recent police success shows the efficiency of Malaysia's internal security apparatus.
Indeed, the ISA is a useful tool for combating potential threats; it allows detention without warrant of anybody deemed a threat to the national security or economic life of Malaysia for up to 60 days. It is also possible for an extension to be granted by the minister for home affairs for up to two years without consultation from the judiciary, and the extension is renewable on an indefinite basis.
Yet although perhaps useful for fighting terrorism, the ISA's continued existence has been a cause for concern among international and domestic human rights groups, which worry about its misuse.
Meanwhile, the security outlook in Malaysia has been quiet, although some incidents of kidnapping in the eastern state of Sabah have occurred over the last few years. However, these are not thought to be motivated by Islamist extremism. Militants are instead known to have moved through the area on their way out of training camps in Indonesian-controlled Borneo.
"There are essentially two types of activity in Sabah," explains Steve Wilford of Control Risks Group, an international security consultancy. "One is kidnap for ransom cash, which has prompted foreign embassy travel warnings, and the other is trafficking after training, although this is happening less now with traffic going through Meluku instead."
However, whilst domestic activity has apparently been dealt with, the problem since has been Malaysians operating abroad. This has attracted some grumbles abroad that Malaysia is a "breeding ground" for militants and allegations in the Indonesian media that funding for terrorist groups has come from Malaysian sources.
This was the image Deputy Prime Minister Najib Razak sought to address soon after the news of Azahari's death.
"It's best to study the underlying causes and not be quick to lay blame on others without any concrete evidence," Razak was quoted as saying by Bernama, the state news agency. "We do not see what is happening as having its root in Malaysia...It's very unfortunate that Malaysians like Azahari Husin and Nordin Top played leading roles in the Jemaah Islamiah terrorist organisation in Indonesia, but these are matters beyond our control."
The Indonesians are not the only ones pointing fingers, however, as Thailand has expressed concerns about possible Malaysian involvement in the recent resurgence of violence in its southern provinces, which lie along the countries' mutual border.
The affair came to a diplomatic head earlier this year with the flight of 131 Thai Muslims to Kota Bahru in the border state of Kelantan. Malaysia sought to examine their claims for political asylum while the Thais claimed that Malaysia was harbouring militants. A war of words ensued, including allegations of Malaysian hands helping in the unrest.
Yet it is unlikely that government interests are stirring trouble in the area. Suspected Malaysian involvement revolves around funding activities from wealthy individuals and, according to some accounts, possible links to the PAS.
Thus far Malaysia has remained, almost conspicuously, incident free. Indeed, as the deputy prime minister was keen to point out last week, the government has actively sought to address security concerns in the region - and has even acted as a mediator during negotiations in the Philippines and in Aceh.
At the same time, some suggest that because Islamic politics has also been allowed a place in the mainstream in Malaysia, this has kept potential radicals away from extremist politics.
Whilst this may also be a factor, it only takes one bad apple to ruin the bunch - and all concerned hope that whatever has kept Malaysia incident-free thus far continues.