The Frenchman, drafted in to replace Kimi Raikkonen - who sustained bruising in a crash during Sunday’s race in Great Britain - hit the front in the final hour as he worked down to a 1m 35.262s.
That was enough to put him a quarter of a second clear of midday pacesetter Daniil Kvyat, who managed 1m 35.544s in the Toro Rosso STR9.
McLaren’s Kevin Magnussen, fastest in the early stages of the day, was three tenths of a second further down the road. The Dane was the busiest man of the day, racking up 91 laps in total - two more than Bianchi - in a programme split between aero and tyre evaluations.
Sauber’s test and reserve driver Giedo van der Garde leapt up into fourth in the closing stages of the day, little over one second behind Bianchi. He brought proceedings to an early close however when he hit the barriers at Copse, triggering red flags that then flew for the final 15 minutes of the day.
"It was a pretty hard crash," he reflected. "All the lights went on so I had to go to the medical centre. They checked everything and I am fine.
"I came out of the corner I had a little snap and I caught it, but then suddenly it went the other way and I lost it completely. It's a pity because we were going quite well today."
Van der Garde added that Sauber had tried "a different programme" in the afternoon as a result of the possible ban on Front-and-Rear Interconnected Suspension (FRIC) systems.
His late surge demoted Mercedes’ Lewis Hamilton to fifth, with the Silverstone race winner posting a best time of 1m 36.680s.
"It wasn't an easy day today; we had great weather but unfortunately had some problems at the start of the day which meant we lost some track time," said Hamilton, who was also delayed by an engine change. "It could have been a lot worse as it could have been raining or we could have even done no laps, but some of the things we've tried in the car feel really positive."
The Briton was followed by Williams’ Valtteri Bottas, Marussia’s Max Chilton and Force India’s test and reserve driver Daniel Juncadella, who was competing in only his fourth F1 session.
Red Bull’s four-time world champion Sebastian Vettel was, like Hamilton, delayed by an engine change. He ended a day dedicated to development work for Pirelli in ninth, ahead of Charles Pic - who spent part of his day trialling the Italian manufacturer's new 18-inch prototype tyres with Lotus.
Caterham's Julian Leal rounded out the order, having lost almost six hours of running time with a CU-H issue - which also prevented the team from running Rio Haryanto as originally planned.
"With the time delay we didn't have a chance to really work on set-up options, but I was quite quickly comfortable with the balance of the car and the way the power came in," said Leal, who is now eligible to apply for an FIA Super Licence after completing more than 300 kilometres in total.
"All day I was on relatively high fuel and if we'd had a chance to do a performance run on the softs I'd have ended up with a quicker time, but overall I'm still pleased with how it went. Obviously today wasn't about times, it was about mileage, learning how to work with the team and start to understand how to maximise the performance of a 2014 F1 car, and I feel like I've made a good step with all of those."
Unofficial Wednesday times from Silverstone
1. Jules Bianchi, Ferrari, 1m 35.262s, 89 laps
2. Daniil Kvyat, Toro Rosso, 1m 35.544s, 55 laps
3. Kevin Magnussen, McLaren, 1m 35.593s, 91 laps
4. Giedo van der Garde, Sauber, 1m 36.327s, 84 laps
5. Lewis Hamilton, Mercedes, 1m 36.680s, 47 laps
6. Valtteri Bottas, Williams, 1m 37.193s, 40 laps
7. Max Chilton, Marussia, 1m 37.359s, 77 laps
8. Daniel Juncadella, Force India, 1m 37.449s, 52 laps
9. Sebastian Vettel, Red Bull, 1m 39.410s, 76 laps
10. Charles Pic, Lotus, 1m 41.906s, 39 laps
11. Julian Leal, Caterham, 1m 42.635s, 51 laps