Forecasters predicted a storm at Augusta and sounded the siren to briefly halt proceedings, just as Woods was charging up the leaderboard.
Birdies on nine and 11 got the former all-conquering World No.1 to five-under and another beckoned on the 12th as he stuck an approach to eight-foot.
But the 20-minute disruption knocked him out of his stride and when play resumed Woods missed the chance to close the gap on the leaders to two shots by sending his putt off-target.
Woods pleased the crowds with moments of joy at the turn and still remains firmly in contention as the adverse weather conditions continue to threaten play.
Fortunately, a large section of the field are finished and unaffected, with Brooks Koepka, Francesco Mollinari and Jason Day tied at the top on seven-under.
Dustin Johnson, Justin Harding and Adam Scott are also one behind at six-under.
For players like Paul Casey, his Masters was already over long before the threat of a storm as he trotted off with a final score of ten-over.
World No.1 Justin Rose is also in serious danger of missing the cut – currently set at three-over – after ending up four-over par following another difficult day.