Bale has been accused of diving in winning the penalty which led to him scoring the equaliser from the penalty spot in Cardiff.
The Tottenham man went on to score a stunning late goal as Chris Coleman's troops came from behind to take all three points and leave Scotland's hopes of qualifying for the World Cup in tatters.
Wigan forward Maloney has jumped to the defence of Bale admitting he did make contact with the winger and he has apologised to his Scotland team-mates for the incident which turned the game.
"The penalty decision swung the game in their favour and I feel awful about that," Maloney told the Daily Record. "I think there might have been a bit of contact, to be fair to Bale.
"It wasn't a challenge as such, he just ran across me and part of his legs touched mine. I don't think he dived. It was just a coming-together.
"I haven't seen it again but I have to be honest - my gut feeling was that he didn't dive. I'm pretty sure I didn't put a challenge in but I think there was some contact.
"It happened numerous times in the game. I tried to track back and help Danny Fox, as that was my job on the night. It's just unfortunate that this one time he got in front of me and when he ran across me he ended up winning the penalty.
"I can only apologise to my team-mates. It's just one of these things that can happen in a match. But it's devastating after the effort that everyone put in and it's something I'm going to regret for a very long time."
Maloney concedes their hopes of reaching the finals could be ended should they fail to beat group leaders Belgium on Tuesday.
"Obviously things are not looking good for us now," added Maloney. "This result tonight has turned a decent start into a bad one. It's not been a great start points wise and now we face a very difficult game in Belgium on Tuesday night.
"Obviously, there is going to have to be a vast improvement. I can't stand here and say that it's over if we lose against Belgium but yes, it'll make it an uphill task if we don't get the win over there.
"We just need to do better as a team. Everyone needs to look at themselves - look within themselves - and come up with a little bit more."