The move was more of a precautionary measure, giving the White Sox captain a two-day break with Monday's scheduled off-day.
"He's had the stiff neck the last couple of days, but he played through it," said White Sox manager Robin Ventura. "I don't think he did it playing.
"But he had it last night for sure, maybe a little the night before. We are just making sure nothing lasts any longer."
Konerko, who also has played with a sore right foot after fouling a ball off of that area, leads the American League with 12 multihit games. He entered Sunday ranked second with a 1.123 OPS and a .679 slugging percentage, while checking in fifth with a .383 average.
Dayan Viciedo was moved from left field to designated hitter in Konerko's absence, with Konerko originally scheduled to start at DH. Kosuke Fukudome was inserted in the lineup in left field.