Application markets such as the Google Play Store and the Apple App Store have become the de facto method of distributing software to mobile devices. While official markets dedicate significant resources to detecting malware, state-of-the-art malware detection can be easily circumvented using logic bombs or checks for an emulated environment. We present a Practical Root Exploit Containment (PREC) framework that protects users from such conditional malicious behavior. PREC can dynamically identify system calls from high-risk components (e.g., third-party native libraries) and execute those system calls within isolated threads. Hence, PREC can detect and stop root exploits with high accuracy while imposing low interference to benign applications. We have implemented PREC and evaluated our methodology on 140 most popular benign applications and 10 root exploit malicious applications. Our results show that PREC can successfully detect and stop all the tested malware while reducing the false alarm rates by more than one order of magnitude over traditional malware detection algorithms. PREC is light-weight, which makes it practical for runtime on-device root exploit detection and containment.