He was examined by Astros team doctor David Lintner and sent to Methodist Hospital for further tests. The Pirates said Jakubauskas would be kept at the hospital overnight for observation. The team was awaiting X-ray results.
The 31-year-old Jakubauskas was called up from the minors on Friday and was making his first start of the season.
Berkman drove a 1-0 pitch back to the mound and it hit Jakubauskas in the head. Jakubauskas fell and the ball bounced all the way back to catcher Jason Jaramillo.
Medical staffs from both teams ran to the mound as Jakubauskas stayed down, repeatedly kicking the dirt in obvious pain. Berkman ran to the mound, joining all of the Pirates infielders.
Jakubauskas was down for almost 5 minutes before he sat up, holding an ice pack and towel against his face. Jakubauskas was taken off the field on a medical cart. He gave a thumbs up to the crowd, who offered a standing ovation.
Right-hander D.J. Carrasco replaced Jakubauskas.
Jakubauskas appeared in 35 games (eight starts) for Seattle last season. The Pirates claimed him off waivers in November.