Werner, a 25-year-old left-hander, was 1-2 with a 5.79 ERA in four starts with Tucson. He started the season with Double-A San Antonio, going 4-8 with a 3.23 ERA in 18 starts.
Werner became the 14th starting pitcher that the Padres have used this season -- the most in the Major Leagues. The Rockies have used 13 starting pitchers.
In 2002 and '09, the Padres used 15 starting pitchers, though that number reflects starts by pitchers after rosters expanded after Sept. 1.
Boxberger has a 3.52 ERA in 15 1/3 innings, with 16 hits and 13 walks allowed to go with 20 strikeouts during two stints with the Friars.
"These guys are still growing," Padres manager Bud Black said of the rookie relievers on the roster. "In Box's case, it was some pitch sequencing, the ball-strike ratio. Those are the things that Brad needs to work on."
That said, Black still envisions a bright future for the 24-year-old Boxberger.
"He'll be a strong factor in our bullpen moving forward," Black said.
The Padres also designated outfielder Jeremy Hermida for assignment on Wednesday. Hermida was hitting .252 with three home runs and 22 RBIs in 44 games with Tucson. He made the Padres' Opening Day roster and hit .250 in 24 at-bats before landing on the disabled list April 28 with a strained left abductor.