Bauer, picked one spot behind Seattle's Danny Hultzen as the No. 3 overall selection in last June's Draft, allowed four hits with no walks and two strikeouts in his second spring appearance as the D-backs improved to 2-4-1.
"I was missing more down in the zone today than I like to," Bauer said. "I like to pitch in the upper half of the zone, and today I was getting the ball at the knees and they were hitting it. You throw the ball down in the zone, it loses effective velocity and they can square it up where when it's up in the zone it gets on them quicker."
Josh Collmenter had been slated to start, but he was scratched due to some tightness in his forearm. Bauer had thrown two perfect innings in his debut last Saturday against the Rockies.
Designated hitter Carlos Peguero hit his third home run of the spring for Seattle in the fourth inning off J.J. Putz, but the Mariners fell to 6-2 in Cactus League play with the loss.
Jason Vargas, who'd thrown four perfect innings in his Cactus League opener last week against the Padres, gave up five runs on six hits in four innings this time out. The lefty gave up a solo home run to second baseman Aaron Hill in the first, and a three-run shot to third baseman Ryan Roberts in the fourth.
"They brought a good majority of their regular lineup, so I figured it was going to be a tougher day," Vargas said. "They've got some experienced guys on that team and some guys that have had success against me in the past, so I knew it'd be a good challenge."
Chris Young added the D-backs' third home run off George Sherrill leading off the sixth, and Rusty Ryal took Hong-Chih Kuo deep in the seventh.
Vargas threw 82 pitches as he continued stretching out in preparation for the Mariners' second regular-season game on March 29 in Tokyo against the A's. He has two more spring starts scheduled before the team travels to Japan.
First baseman Alex Liddi went 3-for-4 with a double, two runs and an RBI for Seattle.
Up next for the D-backs: The D-backs play their first night game of the spring Saturday when they play host to the Mariners at 7:05 p.m. at Salt River Fields. Ian Kennedy, the D-backs Opening Day starter, will be making his second appearance of the spring. Free-agent signee Takashi Saito is scheduled to follow Enright to the mound. It will be Saito's second appearance in a D-backs uniform.
Steve Gilbert is a reporter for MLB.com. Read his blog, Inside the D-backs, and follow him on Twitter @SteveGilbertMLB. This story was not subject to the approval of Major League Baseball or its clubs.