Arrieta suffered a right hamstring injury while throwing a pitch to rookie slugger Josh Bell with one out in the bottom of the third inning.
Arrieta was in immediate discomfort and tried to stretch his leg as his infielders, manager Joe Maddon and a trainer visited the mound.
But Arrieta was in obvious pain as he tried to deliver a warmup pitch and walked off the field slowly.
Kris Bryant hit a pair of doubles in his first two at-bats but was left stranded by Anthony Rizzo.
In the field: Freeman took over at shortstop for Javier Baez, who was scratched from the lineup because of a sore left thumb.
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