Teammates Giniel de Villiers and navigator Dirk von Zitzewitz were fourth-fastest and are currently in fourth place in the overall standings, 02:05 behind new rally leader Sebastien Loeb.
The 275km-long stage was preceded by a liaison of 444km, taking the crews from the Argentine town of Resistencia to San Miguel de Tucuman. The stage itself offered a mix of surfaces, and took place at only 200m above sea level.
Al-Attiyah/Baumel, who won Stage 1 of Dakar 2017 on Monday, pushed throughout the stage, but saw their overall rally lead slip into the hands of Peugeot rival Loeb.
The Toyota Gazoo Racing SA crew is only 28 seconds behind the new rally leader, despite the Frenchman winning Tuesday’s stage by 01:23.