Mini driver Pech maintained his advantage into the final afternoon, with Kubica only able to chip away slightly at his rival's cushion.
But a choice of two studded and two winter tyres for the last stage, where Pech ran slicks, allowed Kubica to go half a minute quicker and seal victory by 19.9s, having been 11.8s down at the start of the stage.
Raimund Baumschlager completed the podium after being part of the lead battle on day one.
Last year's Rally Poland winner Kajetan Kajetanowicz led the early stages on Saturday before crashing.
Leading finishers:Pos Driver Team/Car Time/Gap 1. Robert Kubica M-Sport Ford 2h26m42.4s 2. Vaclav Pech Invelt Mini +19.9s 3. Raimund Baumschlager BRR Skoda +1m38.9s 4. Beppo Harrach DiTech Mitsubishi +3m00.3s 5. Jaromir Tarabus Czech Skoda +3m39.6s 6. Andreas Aigner Stohl Peugeot +4m33.4s 7. Vasily Gryazin SRT Ford +6m27.4s 8. Roman Odlozilik TRT Ford +7m16.3s 9. Robert Consani Delta Peugeot +9m22.2s 10. Hannes Neubauer Stohl Subaru +11m39.6s
The fifth Intercontinental Rally Challenge was the best yet, and it was Skoda UK driver Andreas Mikkelsen who emerged as champion from a tense five-way shootout at the season finale. Matt Beer reviews the season