Seamus Kelleher, one of four debutants as Lowestoft made nine changes for last night's much-delayed Championship Managers Cup tie, came up with a last minute winner at Theobald's Lane.
Joe Jefford, Tom Cole and Jack Smith also made their first senior appearances while coach Craig Fleming and fitness coach Dave Carolan came on for the last 30 seconds after making up the numbers on the bench.
Yet Lowestoft still dominated the first half, taking an 18th minute lead when Stuart Ainsley's free-kick was knocked down for Jamie Godbold to volley home and going close to a second when Jefford was twice denied by goal-line clearances.
Cheshunt levelled in the 77th minute with sub Rod Osei racing clear to shoot into the roof of the net. But Lowestoft snatched victory at the death when Jamie Forshaw made ground down the right before crossing for Kelleher to head home from close range.
The Blues will be at home to Heybridge Swifts in the next round.
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