Victory would have taken the Gunners to the top of the table on Saturday evening.
Speaking after Saturday's draw at the Stadium of Light, he said: "If you have a watch, you can control. It's as simple as that.
"It was outside the four minutes. I know the referee can give more than four, it's a minimum of four minutes.
"But in the four minutes nothing happened to justify the extension of the time. But I cannot do anything about that."
Wenger also denied that he had accosted Atkinson, stating: "I complain to nobody."
The Frenchman could have appealed against the FA's charge, which would have freed him to take his place in the dugout at White Hart Lane.
However, with an independent regulatory commission unlikely to convene a personal hearing before Arsenal face West Brom on Saturday, disputing the charge would have risked suspension for Arsenal's Premier League trip to Chelsea on 3 October.
The touchline ban is Wenger's first in English football since he joined Arsenal in 1996.
However, he had a 12-match suspension overturned on appeal in 2001 after initially being found guilty of "threatening behaviour and physical intimidation" towards fourth official, Paul Taylor, after a defeat at Sunderland.
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