The World No 5 informed WTA supervisor Pam Whytcross in the training room, two hours before she was due to play Taiwanese qualifier Hsieh Su Wei in the quarter-finals.
"We were called into the training room at 2pm and were informed that she had a right elbow injury (nerve problem). It is disappointing but we wish her the best.
"It is still early in the season and players have to manage their injuries carefully," said Pam at the Bukit Kiara Equestrian & Country Club yesterday.
Agnieszka addressed the crowd on centre court and said: "I am sorry I can't continue. Had a great time in Kuala Lumpur and I hope to return in future."
She immediately left the arena for the Kuala Lumpur International Airport to board a flight to Krakow, Poland, to get treatment for her injury.
The 22-year-old reached her career high ranking following her eighth tour victory at the Dubai Championships before heading for KL.
Agnieszka, who had her shoulder and thigh strapped throughout the event, had a problem with the tight scheduling due to the weather condition.
Her first round match with Uzbekistan's Akgul Amanmuradova was scheduled originally for Tuesday before being pushed back to the next day due to heavy rain.
The match was halted once again before it was completed on Thursday afternoon and two hours later, she was back on centre court against Czech Republic's Karolina Pliskova (6-4, 6-4). She complained of a sore shoulder after her second round win.
Agnieszka is due to compete in Indian Wells and Miami.
