"Abu Dhabi is going to be my last race with the team," he told a news conference at the Brazilian Grand Prix, the penultimate round of the championship, without expanding on the reasons behind the decision.
"From my point of view this has been a pretty difficult season but that's secondary to the fact that the team continues and that's the most important thing."
Reports, confirmed by team sources, emerged at the previous race in Mexico that Lowdon and team principal John Booth had handed in their resignations and would leave once the season had ended.
Neither man, both well-regarded in the paddock as motor racing veterans who have been involved in the sport from the junior series upwards, had confirmed the reports.
Lowdon helped secure Marussia's survival after the team, who entered Formula One in 2010 as Virgin Racing, went into administration and missed the last three races of last year.
Stephen Fitzpatrick, who runs the Independent British energy supplier Ovo, then took over as owner in March and has said he was funding the team personally.
Media reports have spoken of differences of opinions between the owner and those running the team, which could yet change hands before the start of next season.
Tavo Hellmund, the Texan-based entrepreneur who is close to Formula One's commercial supremo Bernie Ecclestone and helped Mexico return to the grand prix calendar this year, has expressed an interest in buying the team with a group of investors.
Manor have been racing with year-old Ferrari engines this season, and have not scored any points, but are due to switch to Mercedes power units in 2016.
They qualified for an estimated $50 million in prize money this season after finishing ninth in 2014 thanks to the efforts of their late French driver Jules Bianchi who suffered fatal injuries in Japan last year.
(Reporting by Alan Baldwin, editing by Tony Jimenez)
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