Schumacher announced his decision to step down from driving at the end of the year on Thursday, and had vowed to give his all to end his record-breaking career on a high.
But the German pushed a little too hard and made a costly error at Spoon Curve, dropping a rear wheel onto the grass and skidding into the barriers, eventually winding up 10th-fastest.
McLaren had enjoyed the better of the morning session with Jenson Button leading Lewis Hamilton at the top of the standings.
But Red Bull had not shown their hand in the earlier running, and they looked far stronger in the afternoon.
Mark Webber led the way with a lap of one minute 32.493 seconds to beat Hamilton by just over two-tenths of a second.
Sebastian Vettel, the closest man to championship leader Fernando Alonso in the standings, backed up his team-mate's showing with the third-fastest time.
Nico Hulkenberg raised hopes that Force India can follow up a strong showing in Singapore as he claimed fourth, but it was an awful session for his team-mate Paul Di Resta.
The Scot brought out the red flags early in the session, making the same error Schumacher would later replicate at Spoon Curve, ruling him out of the remainder of the 90 minutes of running and finishing bottom of the timesheets.
Alonso, trying to fend off a five-strong chasing pack in the title race, was fifth-fastest and Ferrari appear to once again be well shy of the pace of McLaren and Red Bull.
Sixth went to Romain Grosjean's Lotus while Button dropped back to seventh after topping the times earlier in the day.
Bruno Senna was eighth, having sat out the first practice session as reserve driver Valtteri Bottas was given some seat time, with Felipe Massa and Schumacher rounding out the top 10.
Nico Rosberg was 11th in the other Mercedes after an engine shutdown at the end of the morning running had forced a change of powerplant.
New McLaren signing Sergio Perez was 12th ahead of Sauber team-mate and home favourite Kamui Kobayashi, who had been as high as second.
It was also a disappointing session for Kimi Raikkonen. The Finn, third in the championship, missed the majority of the session after a KERS issue led his team to inform him his car was "unsafe".
After getting back out during the final moments of the session, he set the 14th-fastest time.
The session concluded with Vitaly Petrov having a scary moment in his Caterham, after the rear wing fell off as he approached the high-speed first turn, but the Russian was unhurt.