"We liked Gregorius better," he told Arizona Sports 620's Burns and Gambo Wednesday.
Towers was discussing the reasoning behind the trade he made the day before, which sent out Bauer along with pitchers Bryan Shaw and Matt Albers in exchange for shortstop Didi Gregorius, pitcher Tony Sipp and first baseman Lars Anderson.
The move has been questioned by many, as the thought of trading Bauer is a tough one to swallow. The pitcher was taken third overall in the 2011 MLB Draft and, while he struggled in a short stint with the D-backs last summer, is still thought of as one of the game's better pitching prospects.
However, Towers said the team needed to add quality depth at the shortstop position, and this was the time to do it.
"Other than Chris Owings we lacked depth in our system," he said. "We didn't want to put all of our eggs in one basket on somebody like Chris Owings, we wanted to have another premier shortstop that we thought was close."
Towers said a look at the free agent market along with who would be available next summer led him to deciding to make a deal for a shortstop now.
"We didn't want to go fishing in those big free agent ponds a year or two from now when you're going to be probably be overpaying for players that the talent doesn't equal the value," he said.
"He could play shortstop in the big leagues right now and be an above average shortstop," Towers said. "And we think the bat is close."
Gregorius will be under the D-backs' control for the next six years, which was something Towers said played a key role in Arizona's pursuit.
It's also one of the reasons why they were willing to part with a player like Bauer, who they valued less than fellow pitcher Tyler Skaggs.
"If we were going to move one of our talented young pitchers like a Trevor Bauer, where there was six years of control, we wanted a young shortstop with six years of control."