Spaniard Garcia, playing his first event in Europe since winning the Masters, shot a two-under 70 on Friday, leaving him eight under par overall.
Sweden's Stenson, the 2016 winner, carded a three-under 69 in his second round as he continued preparations for a defence of his Open title in July.
The pair are a shot behind Swede Joakim Lagergren and France's Joel Stalter.
England's Tommy Fleetwood, who finished fourth at the US Open on Sunday, is tied for 11th, three strokes adrift of the leaders in Munich.
But compatriot Richard Bland moved level with Garcia and Stenson with a second-round 69.
Fellow Englishman Matthew Southgate was one shot further back on seven under par overall.
"I'm not on top of my game by any means but I think it was a good kind of professional fighting display," Stenson said.
"We kept it pretty tidy, anyway, and made a couple of birdies when we had the chances and didn't drop too many. You don't have to be ashamed of three under I guess around here."
Sergio Garcia and Henrik Stenson are one shot off the pace after the second round of the BMW International.