Wenger's men were humiliated at the Allianz Arena, falling to a 5-1 loss in Munich for the second time in as many seasons, despite going in at half-time level at 1-1.
With the 67-year-old's contract set to expire at the end of the season, there is growing speculation Wenger's 21-year association with the club could be coming to an end.
Keown acknowledged his former boss, with whom he won three Premier League and FA Cup titles, had never known times like these.
But while he concedes major changes could be afoot, he insists he would never call for Wenger to be sacked.
"I can't ever say that I'd like to see him go when you've won things," he said on BT Sport. "He's almost my footballing father. You do things as a family.
"But he's an intelligent man and this is obviously his lowest point ever.
"Should he be protected from himself? This is a massive low point for him and will only bring forward the change that looks ever more likely.
"I think it will be him that makes the decision. The realisation [is]... he's probably going to have to hand the reins over to someone else."
Keown was not the only Arsenal alumnus to voice his disappointment with the last-16 first-leg result.
We are a ******g shambles— Ian Wright (@IanWright0) February 15, 2017
At least let it go to the ******g home leg— Ian Wright (@IanWright0) February 15, 2017
**** it !!! Not watching anymore.— Ian Wright (@IanWright0) February 15, 2017
Legendary striker Ian Wright branded the team a "******g shambles" on Twitter before declaring he could not sit and watch any more.