Last year's Monaco race winner Da Costa posted his time in the final eight minutes of the second practice session, following a red flag called for Mahindra's Alexander Sims as he pulled over at the entry of the Rascasse with a broken front-right steering arm.
Sims appeared to have an incident with Nissan e.dams' Sebastien Buemi, which was placed under investigation by the stewards - but was not deemed worthy of any further action.
The British driver kicked off the opening flurry of laps with the initial fastest time, a 1m31.932s, but this was quickly bettered as the Mercedes duo of de Vries and Vandoorne swept to the top, with the former becoming the first driver to tap into the 1m30s.
After a brief yellow flag at the Swimming Pool section as Avalanche Andretti rookie Oliver Askew came to a stop, and will require a powertrain change for qualifying, Robin Frijns then leaped into control at the top, logging a 1m30.678s despite a lock-up at the Nouvelle Chicane.
Championship leader Jean-Eric Vergne then followed him into second with just a tenth in arrears, although it appeared that Lucas di Grassi would leapfrog them both with a pair of fastest opening sectors before a Rascasse mistake neutered his assault on top spot.
Dan Ticktum then brought out a yellow flag at the first corner with a lock-up precipitating a dive into the Sainte Devote run-off, before Sims' incident produced the red flag.
With eight minutes left on the clock after the stranded Mahindra was cleared, da Costa charged to the top, with Mitch Evans going into second place behind him with a two-tenths deficit.
Vergne then looked set to make it a DS Techeetah 1-2 on the timing boards, but hit the wall on the exit of the Swimming Pool complex and had to immediately make a trip to the pitlane to assess the damage.
Evans tried to overturn da Costa's advantage at the death of the session, but got marginally held up by Pascal Wehrlein before going too deep into the Nouvelle Chicane to spoil his lap.
Frijns' earlier timesheet-topping lap was good enough for third, with Vergne classified fourth ahead of Maximilian Guenther.
De Vries ended FP2 in sixth, ahead of Porsche duo Wehrlein and Andre Lotterer, while Edoardo Mortara and Jake Dennis completed the top ten.
Earlier in the morning, de Vries had headed the first practice session with a 1m31.154s, which withstood a late charge from Nick Cassidy as the Envision driver locked up at the Rascasse on his final lap before the chequered flag.
Cassidy thus slotted into second, going 0.118s slower than the Mercedes driver's time - and beating Edoardo Mortara by just over three tenths. Da Costa was fourth fastest in that session, beating Buemi and Lotterer.
Formula E Monaco E-Prix - Practice results
FP2
FP1
