With rounds of 69 and 78, Lahiri finished at three-over 147 and missed the cut, which fell at one-under. He had a solid first round of 69, but with the weather worsening by the hour in the afternoon, he was left struggling on the second day.
It was the second successive year Lahiri missed the cut at Houston.
Lahiri, whose only top-10 finish this season has been in his home country, where he was tied-second at the Hero Indian Open last month, will now tee up at the Masters for the second year running. In 2015, he made the cut on his Augusta debut and finished tied 49th.
About 45 minutes after Lahiri finished, there was darkness and play was suspended with 27 players needing to come this morning to finish their second round.
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First-round leader Charley Hoffman followed an eight-under 64 with a two-under 70 yesterday to move to 10-under 134 and a one-stroke lead over Jamie Lovemark.
Hoffman has made the cut in each of his 10 starts at Houston Open.
Lovemark, a former NCAA champion, is seeking his first PGA TOUR title after having his career affected by back surgery. He was one of four players to shoot the day's low score, 68, under conditions that worsened as the afternoon went on.
Jordan Spieth (67-73) was tied 20th, while Rickie Fowler was tied 12th with rounds of 69 and 70.
The second round, which was suspended for 93 minutes in the day and later due to darkness last evening was finished this morning.
As 81 players out of 144 professionals made the 36-hole cut at one-under-par 143 or better, there will be a 54-hole cut for 70 players and ties after the third round.