Alexander Volodko swept the visitors in front with just six minutes on the clock with a superb lofted finish over Mickael Landreau, and further goals from Vitaly Rodionov and Edgar Olekhnovich effectively ended the contest before half-time.
Aurelien Chedjou reduced the deficit just before the hour mark but despite dominating for long periods Lille were faced with another defeat to heap more pressure on boss Rudi Garcia after a poor start to their Ligue 1 season.
The hosts had started in promising fashion, Salomon Kalou bringing a save out of BATE goalkeeper Andrey Gorbunov with less than four minutes on the clock, then Florent Balmont firing wide from 12 yards.
Volodko provided a beautiful finish to a cross by Maksim Bordachev to put the visitors in front two minutes later, but Lille still looked threatening and Tulio De Melo headed just over the bar with nine minutes gone.
Mathieu Debuchy brought another save out of Gorbunov but Lille's pressure came to nothing as the visitors increased their lead in the 20th minute when Rodionov scored with a low shot after Alexander Pavlov's neat ball from the left.
The French side responded well, Gorbunov punching away a free-kick from Dimitri Payet then Debuchy firing wide, then Payet saw another effort blocked in the box by Marko Simic.
BATE rounded off a remarkable half by making it 3-0 two minutes from the break when Olekhnovich drilled home from 12 yards, but Lille had time to press again with Gorbunov saving from Payet.
Kalou and Debuchy maintained Lille's pressure early in the second half before the hosts finally made their breakthrough in the 59th minute, Chedjou meeting a Payet corner from the left to head past Gorbunov.
Pushing forward, Lille continued to dominate possession with Payet firing over and Ryan Mendes De Graca also shooting wide.
Gorbunov saved from Payet and Balmont, and Kalou headed a fine chance wide from six yards, as the visitors held on to their advantage to record a flattering win.