Manchester City striker Emmanuel Adebayor and Salifou were amongst the travelling party but were not injured, although O'Neill admits the Villa midfielder was in shock.
"He's obviously very shaken up but he's fine," he said. "He's unhurt but pretty upset by it all - but physically he's okay."
Asked if he ever expected an incident such as this, O'Neill added: "No I didn't. I know that there was an incident with the England cricket team not so long ago I think in Sri Lanka, there was certainly a cricketing incident.
"But I wasn't really expecting anything like this at all.
"So as I said he's pretty shaken but he's unhurt and that's the most important thing."
Togo are scheduled to start their cup campaign against Ghana on Monday, although their participation in the tournament is now in doubt.
O'Neill would not be drawn on whether he thinks Togo should pull out of the competition, but hopes to see Salifou return to Villa Park soon.
"That's a decision for them to make (to carry on in Angola) but I'd love to see Moustapha back," he remarked.
"He's a great character and he's very, very popular with the players."
Villa's scheduled Premier League game against Wigan on Saturday has been called off due to a frozen pitch at the DW Stadium.
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