Soosay was suspended last month by the AFC after Malaysian media reported an official at the 46-member confederation had been asked by Soosay to "tamper or hide" documents during a 2012 external audit.
The PricewaterhouseCoopers inspection came following the lifetime ban handed out to former AFC president Mohammed Bin Hammam, by world governing body FIFA for ethics breaches, who Soosay worked closely with.
"The Asian Football Confederation would like to thank Dato’ Alex Soosay for his commitment to Asian football during his extensive 20-year-long career at the AFC and wishes him all the best for his future career," the AFC said in a statement.
The AFC did not say if the findings of the Soosay investigation would be made public. The body has also resisted calls to make public the 2012 audit.
Soosay's deputy Windsor John will take over the role until a new general secretary is appointed, the body said.
A former player, Soosay held the position of AFC general secretary since 2008 following the retirement of his Malaysian compatriot Peter Velappan.
He worked under Bin Hammam but his position appeared fragile when Shaikh Salman bin Ebrahim Al Khalifa, an outspoken critic of the Qatari, was elected AFC President in 2013.
In April, the Malay Mail said it had obtained video evidence in which AFC financial directory Bryan Kuan Wee Hong had told investigators in 2012 that Soosay had come to him for help.
"He said based on (what) they have found out, 'have I committed any crime and will they blame me for anything? Anything that you have... is it possible to either tamper or hide it somewhere?'," Kuan said of his conversation with Soosay.
Soosay told Reuters after the AFC Congress in Bahrain in May the "case is closed" blaming election fever for the matter becoming public. Salman was elected unopposed for another four-year term at the regional meeting.
Soosay is the latest in a long line of casualties at the AFC since the Bahraini came to power.
Former Bin Hammam allies Manilal Fernando of Sri Lanka, banned for life by FIFA for bribery, and Thailand's Worawi Makudi have both been voted out of the world governing body's executive committee in Salman's tenure.
(Writing by Patrick Johnston in Singapore; editing by Amlan Chakraborty)
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