Teenage defender Josh Jirbandey scored his first goal for Lewes but a reply in first-half stoppage time ensured the teams went in level at Ebbsfleet.
There was a worrying moment for Ebbsfleet in the 14th minute when Darius Charles bundled over Tim Rivers as he appeared to be in behind the defence but the home skipper escaped with a booking.
Lewes were more than a measure for their opponents at this stage, restricting Ebbsfleet to a single chance for Michael West which Rikki Banks held easily.
The Rooks threatened to break the deadlock on 34 minutes through Chris Breach, the scorer of their winner against Weymouth on Saturday. Michael Standing sent over a teasing free-kick from the right which Breach directed just wide of the far post with a diving header.
Ebbsfleet made a change on 36 minutes, taking off former Crawley defender Sacha Opinel who looked in danger of a red card after three fouls on David Wheeler.
A minute later Luke Rooney threaded a pass in behind the defence for Rivers who miscued a shot past the near upright.
Lewes were creating the more chances and Luke Rooney had a 20-yard effort touched over the bar by goalkeeper Lance Cronin.
The pressure paid off four minutes before the break when Standing delivered a corner from the right which Jirbandey met at the near post with a right-foot volley into the top corner.
In the third minute of injury time Chris Breach was penalised right on the edge of the penalty area when it looked like he had been fouled. Rashid Yussuff's free-kick came back off the wall but he buried the rebound low into the bottom corner.
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