Portugal, who rested captain and leading scorer Cristiano Ronaldo after he played in Saturday's Champions League final for Real Madrid, went ahead through an Andre Silva header from Ricardo Quaresma's pinpoint cross in the 22nd minute.
Midfielder Joao Mario doubled the lead when he rifled in a shot from outside the penalty area and Portugal, who face Spain, Morocco and Iran in their World Cup group, seemed to be in control.
The cracks began to appear five minutes later, however, when Anice Badri was left alone inside the penalty area to fire past Anthony Lopes and pull one back for Tunisia who face England, Panama and Belgium in their World Cup group.
Portugal's defence imploded in their previous game, a 3-0 friendly defeat by the Netherlands in March, and gave coach Fernando Santos more cause for concern in the 64th minute.
They failed to properly clear a free kick and when the ball was played back in, Fakhreddine Ben Youssef got between four defenders to slide the ball home with the hosts appealing in vain for offside.
(Writing by Brian Homewood in Bern, editing by Ed Osmond)
