The 21-year-old winger was forced off midway through the first half of the 5-0 win over Nottingham Forest on Sunday.
This was after taking a kick to the ankle.
The injury came just over three weeks before the World Cup begins in Qatar.
“Bukayo just missed one or two (training sessions) and he was fine today,” Arteta said. “We’re using our brains and our common sense, but obviously he had a kick.
“He was uncomfortable with it.
“We made the decision to get him off and now he’s feeling fine.”
Arteta was involved in a heated touchline debate with both Saka and club doctor Gary O’Driscoll, and explained Saka was trying to play through the pain before the decision was made to take him off.
“The conversation was easy – ‘He’s in, or he’s out’ – but in between we can’t have a player (injured) for five, six, seven minutes,” Arteta said.
With the World Cup imminent, Arteta is keen to keep focus among his players on Arsenal duty as they battle to top their Europa League group and stay in first place in the Premier League.
“Every day I feel responsibility to protect them, to guide them, to get the best out of them,” he said. “But we are playing for Arsenal at the moment and that’s what they have to focus on.
“When they played for England or their national teams they have to focus on the national team and on England and this is what we have to.”