The Italian had been down in ninth position heading into the final two minutes, his session compromised by an early off at Turn 13 which dragged gravel into the front of his car.
In his absence Yvan Muller and RML Chevrolet stablemate Tom Chilton had led the way, with Muller fastest on a 2m12.411s.
Tarquini, fastest in the first session, was not to be denied a practice sweep, however.
One final run produced a 2m12.228s, earning him top spot by just under two tenths of a second.
Muller and Chilton stayed second and third, while defending champion Rob Huff showed strongly again by taking fourth in his Munnich SEAT.
The Spanish marque won the opening race in Slovakia last year courtesy of Tarquini.
Tiago Monteiro made it two Hondas in the top five, although he was forced to abandon his fastest lap when Alex MacDowall went off at Turn 13, bringing out the yellow flags.
It was just one of a number of incidents in a messy session, with James Nash, Rene Munnich, Marc Basseng, Charles Ng, Fredy Barth and Franz Engstler also enjoying lurid moments.
Munnich’s off prompted the reds to fly, with his SEAT beached at the exit of Turn 9. He was pushed out and able to return to the pits under his own steam.
Darryl O’Young backed up his FP1 pace by going sixth fastest – the top BMW – although he was more than 1.7s down on Tarquini.
Norbert Michelisz in the Zengo-run Honda Civic was seventh, while Tom Coronel’s ROAL BMW was sandwiched by the SEATS of Fernando Monje and Pepe Oriola.
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