Upton immediately fell to the ground but did not stay down long. After being examined by the team's training staff, Upton remained in the game and scored from first base when Miguel Montero followed with a double to right-center.
However, Upton did not come out for the top of the second as Gerardo Parra moved from left field to right field and Cole Gillespie took over in left. The team said Upton exited for precautionary reasons after feeling nauseous while running the bases.
"Justin got hit on the bill of his helmet, thank goodness it was a glancing blow than a direct blow," Lee said. "Neurologically, he looked great on the field according to the trainers, no loss of consciousness, had no loss of memory."
Upton is listed as day to day.
"Passed everything with flying colors," Lee said. "No major concerns, but to be cautious, we kept him out of the game and then did a CT scan this afternoon which was completely normal. We'll just do further testing [Monday]. He's day to day at this point, but we don't have any major concerns. He looks very, very good."
Upton will undergo an ImPACT neurological test Monday to determine if there are any lingering effects. Each player undergoes the test during Spring Training to form a baseline result that can be compared to in cases like this.
Upton is tied with the Nationals' Danny Espinosa for the National League lead in hit-by-pitches with 19.
Lincecum walked to the plate to check on Upton and later sent word to him that the pitch was completely unintentional, and he hoped that he would be OK.
"There was no intention of doing that," Lincecum said of hitting Upton.
"You definitely feel for Lincecum because you can tell right away there was nothing intentional there," D-backs closer J.J. Putz said.
Steve Gilbert is a reporter for MLB.com. Follow him on Twitter @dbackswriter. This story was not subject to the approval of Major League Baseball or its clubs.