Federer cruised through the deciding set to win 6-4 3-6 6-1 against the 35-year-old German in his first match since his Australian Open last-16 exit.
The 20-time Grand Slam champion, 37, has never lost to Kohlschreiber, winning all 14 of their meetings.
Federer is again going for a 100th ATP singles title after moving on to 99 at the Swiss Indoors in October.
Federer, now ranked seventh in the world, is second in terms of all-time ATP victories, with only American Jimmy Connors in front of him on 109.
He is going for a record eighth title in Dubai, which has served as his off-season training base for several years.
Earlier this month it was confirmed he will make his return to clay - having not played on the surface since 2016 - at the Madrid Open in May.
Meanwhile, Russian fourth seed Karen Khachanov and Canadian seventh seed Milos Raonic suffered first-round defeats against unseeded opponents on Monday.