The 2011 champion struck four birdies on the front nine to turn in 31 and suffered his only blip on the par-four 10th when he went one over, but recovered with two more birdies on the 11th and 13th holes.
"It's unbelievable," Lewis said. "I'm so happy, it's been a rough ride but this week I played hard. I obviously got off to a bad start, to finish the way I've been finishing has been brilliant so I'm happy."
Herbert led for three days in Portugal but was found wanting when it counted most, bogeying his second hole of the afternoon.
The Australian managed to turn in one-under and added another birdie on the par three 13th, but finished poorly, going two strokes over on the last hole to sign for 71.
Pepperell started the day three-strokes behind Herbert and had six birdies offset by two bogeys, including one on the 18th hole, to close with a four-under-par 67 and a share of second place.
Sergio Garcia ended his warm-up for next week's Ryder Cup with an error-free 65 that included a stunning eagle on his first hole of the day.
The Spaniard, who will line up for team Europe against the United States at Le Golf National in Paris finished on 15-under for a share of seventh place in a group of five players, including Oliver Fisher.
Englishman Fisher, who became the first player to card a sub-60 round in European Tour history when he signed for 59 on the second day in Vilamoura, closed with a 70 that included a mixed bag of four birdies and three bogeys.
(Reporting by Simon Jennings in Bengaluru, editing by Pritha Sarkar)
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