The 30-year-old former Wales centre played on until the 33rd minute after being tackled by Deacon Manu in the first minute of the 23-17 loss, but was then taken to hospital for X-rays.
He underwent further tests on Sunday and has now been ruled out for the start of the Aviva Premiership season, with Welsh facing Leicester on September 2.
A club statement read: "London Welsh can confirm that Gavin Henson suffered a minor fracture to his cheekbone during London Welsh's pre-season friendly with the Scarlets at Parc y Scarlets on Saturday.
"It is anticipated that Gavin will return to full contact training in six weeks."
Head coach Lyn Jones had tried to remain positive on Saturday about the prognosis of the high-profile new signing.
"We're hoping for the best, but if it's the worst he's not the first player to get injured and we'll just have to be patient and deal with it," Jones said.
"These are things you've got to deal with in rugby. You've got to deal with thunderbolts all the time.
"No player wants to get injured in a pre-season friendly because it's hugely frustrating because of all the hard work that's been done leading up to the start of the season."
The Exiles last month handed Henson yet another chance to resurrect his career. He had been without a club since April, after being sacked by Cardiff Blues over his drunken behaviour on a flight returning from a game in Glasgow.
Henson previously worked with Jones during his time at the Ospreys, producing arguably the best rugby of his career and helping the region win two Celtic League titles and an Anglo-Welsh Cup.
Henson won the most recent of his 33 Wales caps in the World Cup warm-up victory over England in Cardiff last August, but a wrist injury sustained in that game denied him the chance to be involved in the World Cup in New Zealand.
Given the player's history the move will be considered by many to be a risky one for London Welsh as they prepare to embark on their first top-flight campaign.
Despite playing an integral part in Wales' 2005 and 2008 Grand Slam campaigns, and touring New Zealand with the British and Irish Lions in 2005, Henson has yet to deliver consistently on the glimpses of class he has shown during a checkered career.
The Blues were Henson's fourth club in little over a year after being released by the Ospreys in 2010 and having short stints at Saracens and Toulon.
His spell in France had also been marred by an alcohol-related incident, with the club suspending him for a week after a nightclub altercation with two team-mates.
During a period of unpaid leave from the Ospreys prior to his move to Saracens he also appeared on reality TV shows Strictly Come Dancing and 71 Degrees North, and last year featured on The Bachelor.