The Paraguay forward came close to joining the Serie A outfit but the deal fell through earlier this week.
Despite also being linked with Fulham, the 29-year-old Santa Cruz remained at Eastlands.
"It's not a disappointment," said Lotito. "We decided to take some time and wait for the winter transfer market in order to evaluate whether to make that signing, considering that in that role we already have Mauro Zarate, Sergio Floccari, Tommaso Rocchi and Pasquale Foggia."
Zarate was a reported target of Tottenham but Lotito has reiterated the South American striker will remain with the Romans for a long time.
"I don't consider offers for Zarate because the Argentinian is not for sale and is a key player for this club," said Lotito.