Lahiri, who had a disappointing six-over 76 on first day, was three-over 38 for the first nine, which was the back nine of the course.
He had doubles on Par-4 15 and Par-4 18th and that damage alone was ruin his chances. He also had a bogey on 12th and a birdie on 13th. Two birdies and seven pars on the second nine were not enough. He totalled seven-over 147 while the cut fell at three-over 145.
He has now missed cut at the PLAYERS, AT&T Byron Nelson and now Dean & Deluca, where he had finished sixth in 2016. Lahiri will play the Memorial next week.
Meanwhile, Jordan Spieth, who is coming off two consecutive missed cuts, redeemed himself as he recovered from a bad start by going five-under over his final 13 holes at the Colonial on Friday.
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His two-under 68 put the defending champion at 2-under 138, four shots behind second-round leaders Webb Simpson, Kevin Kisner, Danny Lee and Scott Piercy.
Masters champion Sergio Garcia (66) and fellow Spaniard Jon Rahm (69), who played in the same group, were at five- under along with England's Paul Casey (66) and Sean O'Hair (68).
Garcia had six birdies, while Rahm didn't get his first until 17 while finishing with two straight.
Phil Mickelson didn't have a birdie while shooting a 75 that left him at 2 over, three shots clear of the cut in his first Colonial since the two-time champ missed the cut in 2010.