The 27-year-old injured his left knee at a ruck in front of his own posts when he was cleaned out in the 48th minute and director of rugby Todd Blackadder says the initial signs are not good.
He said: "I hope it's not the same knee as he injured last season, but it doesn't look good."
Faletau, who suffered a medial knee ligament injury in January this year, will now be sent for tests to determine the extent of the problem and the club, along with Wales, will be hoping for good news.
Bath ended up losing the Champions Cup match against Toulon 24-20 after France international Anthony Belleau produced a moment of brilliance in the dying stages to snatch a win.
That defeat leaves the English outfit second in Pool 5 whilst their French rivals are sitting in first on 12 points, having won all three of their matches.