Arruabarrena – who won the tournament for her first title in 2012 – prevailed 7-6 (7-4) 6-1 to reach the Bogota quarters for the sixth time in her career.
The Spaniard trailed 5-2 in the opening set, but she rallied to eventually outlast her Italian opponent on the Colombian clay.
"She actually started playing really well, hitting super hard and putting all of the balls in," 11th seed Arruabarrena said. "I just accepted that, and I was playing solid myself. In the end, I managed to turn it around and win again."
After needing almost one-and-a-half hours to win, Arruabarrena will face fifth seed Tamara Zidansek for a place in the semi-finals.
Slovenian Zidansek was a class above Sachia Vickery, cruising to a 6-2 6-0 victory in the round of 16.
Elsewhere, 2012 French Open runner-up Sara Errani blitzed Bibiane Schoofs 6-2 6-1 and eighth seed Magda Linette lost 6-4 6-3 against Astra Sharma.