The 26-year-old Russian, who was playing his first tournament since last August, eliminated third-seeded Nikolay Davydenko in the first round before he fell to 31st-ranked Rochus 7-6 (7-5), 6-4.
Safin, who won the Australian Open last year, was hampered by a knee injury for the past six months leading his ranking to slip to 53 in the world.
The former US Open champion, who seemed frustrated during his match throwing his racquet more than once, blamed his long injury layoff for his defeat yet vowed to keep on working hard to regain his top form.
"It was a lack of matches," the Russian star was quoted as saying by BBC Sport.
"You need to get the rhythm back, it doesn't come straight away. There's still a long way to go and many things to work on.”
Rochus next takes on another Russian, Mikhail Youzhny, who beat his compatriot Igor Andreev.
Meanwhile, fourth-seeded Andre Agassi also suffered a stunning defeat to world number 79, Bjorn Phau.
The American veteran, currently ranked ninth in the world, started his Dubai campaign with an impressive win over Greg Rusedski yet lost his rhythm against Phau, who won 7-5, 7-5 to set up a quarter-final clash with Rainer Schuettler.
"The ball was really flying tonight," said Agassi. "I never got comfortable with my range. I couldn't make three or four shots in a row.”
"I was pressing with the first couple of shots but once I let him use his legs it was a pretty uphill battle after that,” the eight-time Grand Slam champion added.
In other second round action, Roger Federer edged past Kuwaiti wild card Mohammed Al Ghareeb 7-6 (5), 6-4, while Tim Henman upset seventh-seeded Radek Stepanek, to book a last-eight meeting against second-seeded Rafael Nadal.