Front row forward Rowntree limped off in the first half while flanker Moody failed to emerge after the interval, raising concerns over their chances of joining the tour to New Zealand.
But Tigers head coach John Wells said: "Graham hurt his knee and will be out for the rest of the season. He is expected to be back in three or four weeks, so he should okay for the Lions.
"Moody damaged his medial ligament and we believe he will be out for two or three weeks, but we'll just have to wait and see."
However, the duo will miss the remainder of Leicester's Zurich Premiership title bid, compounding a miserable day for the club who saw their hopes of booking a fourth European Cup final appearance dashed at the Walkers Stadium.
They paid the price for squandering two glorious chances in the first half with Ollie Smith and Darren Morris spilling the ball with the line beckoning and the match finely poised.
Wells said: "Having Graham and Lewis in the side certainly gives us something extra but we can't blame their exit for the defeat. We had two opportunities while they were on the pitch but didn't take them.
"Toulouse had only a few chances but took them. There were a fair few points which went begging and you can't do that against a class side like the one we faced today."
The boot of fly-half Andy Goode kept Leicester in the hunt until Jean-Baptiste Ellisalde's 50th-minute try saw Toulouse step up a gear as they wrestled control from the wasteful Tigers.
The French giants, beaten finalists last year who will now face Stade Francais in the competition showpiece on May 22, then crossed again through Frederic Michalak. Finau Maka ran in the first try in the third minute.