The young Austrian set his best time just before the session was red flagged after Pietro Gandolfi spun off at Clark Curve with 5 minutes to go.
The restart led to a frantic shootout, with the majority of the cars taking to the circuit for one last shot at pole. Andy Soucek took full advantage to leap up the leaderboard and take second place, missing the top spot by just 13 thousandths of a second.
Sebastian Hohenthal took an impressive third with the top three being separated by just 0.017s. Henry Surtees was fourth, ahead of Mikhail Aleshin and the late charging Kazim Vasiliauskas respectively. Robert Wickens and Jousse will line up together on row four, whilst Mirko Bortolotti and MiloÅ¡ PavloviÄ‡ rounded out the top ten.
Julien Jousse crashed heavily at Sheene Curve shortly after setting his fastest time of the session and took no further part, having sustained significant damage to the rear of the car. MiloÅ¡ PavloviÄ‡ ended qualifying in the barriers at Hawthorn Bend after crashing heavily at the quickest corner on the circuit.
The top 13 drivers were separated by less than half a second and the top 17 drivers were covered by less than a second.
Philipp Eng said: "It was obviously a very good lap. To get my first pole position is a very special thing – I think it was the first qualifying session where I got everything together."
Andy Soucek said: "I was using a strategy, but I think it was a big mistake! We were waiting for people to put the rubber down on the track – we thought the end of the session would be the best time to go out. I think it was an amazing performance."
Sebastian Hohenthal said: "Coming back to the UK felt very good. Obviously it would have been good with pole, but I know for sure that pole has an uphill start whereas third has downhill! I started off this season setting targets and it went very bad, so I'm just taking it lap by lap and seeing what we can do. It feels good knowing that we can be quick when everything works well."
Qualifying two will take place at 9:45am tomorrow (Saturday), before the opening race of the weekend commences at 2pm. Race two will take place at 12:45pm on Sunday.
FIA Formula Two Championship Qualifying One – Brands Hatch, UK:
1. Philipp Eng, 1:17.445s
2. Andy Soucek, +0.013s
3. Sebastian Hohenthal, +0.017s
4. Henry Surtees, +0.102s
5. Mikhail Aleshin, +0.215s
6. Kazim Vasiliauskas, +0.220s
7. Robert Wickens, +0.278s
8. Julien Jousse, +0.304s
9. Mirko Bortolotti, +0.308s
10. Milos Pavlovic, +0.371s