The visitors had the ball in the net in the 18th minute, with Danny Lafferty's header disallowed for pushing, but aside from that they had very few clear-cut chances and did not force Malta goalkeeper Andrew Hogg to make a serious save.
In contrast, Northern Ireland keeper Alan Mannus, standing in for the ill Roy Carroll, made two terrific second-half saves from Malta captain and former Coventry striker Michael Mifsud.
O'Neill said: "It was a difficult game in that the conditions weren't particularly conducive to trying to play. The pitch was difficult, very bumpy, the wind obviously didn't help matters.
"But overall, whilst we never really seemed in any great danger and we controlled large portions of the game, we didn't create enough chances.
"They were very well organised and at times we played into their hands a little bit with our choice of passing. I think at times a little bit of our inexperience in certain areas of the team showed up tonight [Wednesday]."
The draw took O'Neill's record to eight games without a win since taking over from Nigel Worthington late in 2011, while Northern Ireland have not won a game since beating the Faroe Islands in August of that year.
They have particularly struggled away from home and remarkably their last goal in an away friendly came in a win over Finland six and a half years ago.
"You want to win games, simple as that," said O'Neill. "We've had eight games, we've had five draws and three defeats. We've had some very difficult games in there.
"Of course it's a concern but at the end of the day the only people who can change that are myself and the players and I'm aware of that."
Lafferty met Chris Brunt's corner with a firm header at the back post but Bulgarian referee Nikolay Yordanov appeared to penalise a Northern Ireland player in the centre of the box.
O'Neill said: "I've not seen it again. Obviously if you score at that time in the game it gives you a nice foothold. It was a difficult one. He blew very early, which would suggest that he obviously saw a foul.
"That was disappointing because I think a goal would have settled us down. A number of the younger players I think struggled tonight [Wednesday] and hopefully the experience of tonight [Wednesday] will help them going forward."
O'Neill selected his team with next month's World Cup qualifier against Russia in mind, when Kyle Lafferty and Chris Baird are suspended.
Both were left at home and O'Neill gave Alex Bruce a debut in the holding role in midfield with Walsall's Will Grigg winning his second cap as a lone striker.
The manager gave a positive assessment of both players' performances, saying of 21-year-old Grigg: "I thought he worked very hard. The couple of half-chances he had he maybe could have done a little better with them but overall we're pleased.
"He's a young player playing League One football. We're asking him to come and play international football and, whilst he's adapting to it and I think he's got a very bright future, it was a big ask for him tonight [Wednesday].
"I was pleased with Alex. I saw him play on Saturday against Millwall in that holding role and he played very well. It was important we saw Alex in there tonight [Wednesday]."
Hull defender Bruce, the son of Tigers boss Steve, was a controversial pick given he has previously played for the Republic of Ireland, but he was given a warm reception by the travelling fans when he was substituted late on.
That may not be the case if he plays at home against Russia, but O'Neill said: "It's no concern to me.
"He's available to me. Of the 30 players I have to choose from, I can't afford not to select one on that basis. Alex will come under consideration the way he would always do."