The Timer is the same thing that you know from practically every Fighting Game in existence. In a standard game of KOF, the Timer starts at 60 at the beginning of a Round and counts down to 00, in real time. When the Timer reaches zero and no character has been defeated, the character with more total life at the end is deemed victorious.
So what happens if both characters have the exact same amount of Life left? The game is considered a draw and both characters "lose". If both players were on their last character, then a sudden death round occurs with the same characters both at 300 life (30% of a life bar) and the timer set to 30 seconds. If there is another draw, both players "lose" the match.
Neomaxes tend to last a long period of time and can drain a decent amount of timer before they complete when they connect. As a result, players may be afraid to land a Neomax near the end of the round, worried that the animation won't finish before the time runs out.
It turns out this fear is unjustified. Neomaxes actually will always complete. If you connect, for example, Kyo's Ura 111 Shiki : Ama no Murakumo right when the timer reaches 1, as the Neomax goes on, the clock will go down to zero and then actually just stay at zero until the Neomax finishes! Only after it completes does the match end, either with a K.O., or by the game judging a winner based on remaining life. Since any Neomax that connects is guaranteed to finish before a match ends, don't be afraid to try and connect one close to the end of a round to squeak out a comeback victory.