The e.dams Renault driver posted a 1:30.513s in the morning running before tricky wet conditions prevented an opportunity for the field to topple the Frenchman.
Prost, who was able to successfully test the higher 170kW race mode, ended the day 0.3s quicker than his team-mate Sebastien Buemi, with Dragon Racing's Jerome D'Ambrosio edging Mahindra's Bruno Senna to third.
“Last week we were a bit lost but the last two days from my side have been really positive,” said Prost.
“We had a really, really good pace. I'm quite happy but not over-confident as Abt was looking really strong, Sam Bird is looking strong. Reliability for us has been good too.
“For me and my driving style I think it's better to have more power. It makes it a lot nicer to drive. 170kW makes it more challenging.”
Prior to the test session Formula E teams and drivers held a minute's silence as a mark of respect to IndyCar star Justin Wilson, who succumbed to a severe head injury yesterday.
Andretti Autosport, who Wilson joined for the Russian round in June, reverted to their season one power train after encountering issues with its new system.
As a result, latest recruit Simona de Silverstro and Robin Frijns were both able to log a string of lap times.
Frijns finished eighth with de Silvestro 11th fastest, while Trulli GP's new car completed its first installation lap.
The second Formula E season is due to begin on the streets of Beijing on October 17.
Result: FIUA Formula E Test Day 6, Donington Park
|DS Virgin Racing
|Simona de Silvestro
|Nelson Piquet Jr
|Abt Audi Sport