After Gary Hooper scored his second goal four minutes into the second half to put Celtic 2-0 ahead, a fan ran from a stand for home supporters and tried to attack Lennon by the dugout.
The fan was eventually wrestled away by stewards and police but the incident sparked more crowd trouble as Celtic fans clashed with stewards.
"Clearly this kind of behaviour from supporters is wholly unacceptable," Scottish Football Association chief executive Stewart Regan said in a statement.
"The safety of players, club officials and match officials is paramount on or around the field of play and this clear breach of security is a matter I will be discussing with SPL chief executive Neil Doncaster tomorrow."
The incident was the latest in a succession of problems for former Northern Ireland and Celtic captin Lennon, who has received death threats on several occasions and retired from international football because of them.
A package containing bullets was intercepted last month at a sorting office in Northern Ireland, one of a series of suspicious packages that have been addressed to him.
Celtic's victory kept the Scottish Premier League title race alive going into Sunday's final round of fixtures when they host Motherwell. Their arch-rivals Rangers, who visit Kilmarnock, are one point ahead but with an inferior goal difference.
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