The Rainforest Alliance announced the move on Thursday against James Finlay (Kenya) Ltd and Ekaterra Tea Kenya Plc, meaning that tea sold by them can no longer carry the NGO's certification.
The decision - initially effective for three months - means the companies cannot sell or ship products with a Rainforest Alliance Certified claim.
The alliance - one of the major certification bodies for sustainable development products - said it had launched an investigation after a BBC documentary in February highlighted claims of widespread sexual abuse on tea estates in Kenya, one of the world's biggest tea exporters.
More than 70 women had told the BBC that they had been sexually abused by their supervisors for years.
"For both tea estates, the audits confirmed the presence of non-conformities of the social and management criteria of the Rainforest Alliance Sustainable Agriculture Standard," the alliance said in a statement announcing the suspension of its certification for the two companies.
"The Rainforest Alliance remains committed to doing its part to help stop sexual harassment and gender-based violence in global supply chains. The safety and well-being of women - and of all workers - is an integral part of our certification programme and our mission at large."
Kenyan prosecutors and lawmakers had said in February they would be investigating the accusations but no judicial action has been taken.
The BBC documentary focused on dozens of victims who said they had no choice but to give in to managers' sexual demands or lose their jobs.
One was reportedly infected with HIV by her supervisor, while others fell pregnant.
One supervisor was accused of raping a 14-year-old girl who was living on site at one of the plantations.
Both companies vowed to pursue independent investigations into the allegations.
Unilever last year completed the sale of its global tea business Ekaterra, including the brands Lipton and PG Tips, to CVC Capital Partners in a deal worth 4.5 billion euros ($4.8 billion).
Earlier this month, Sri Lankan conglomerate Browns Investments agreed to buy the James Finlay business in Kenya.
The East African country last year exported more than 550,000 tons of tea, according to latest government figures.