There is an increasing interest in the affine formation control of multi-agent systems, because it can change the centroid, orientation and scale of the formation by controlling only a few leaders. In this paper, the fault-tolerant affine formation control problem is addressed for double-integrator multi-agent systems with partial loss of efficiency and bias faults. Firstly, in order to track the leaders with dynamically changing accelerations, an acceleration observer with prescribed time convergence is proposed, which can estimate the ideal acceleration for each follower. Then, based on the acceleration observer, a fault-tolerant control algorithm is given. A new Lyapunov function candidate is constructed, based on which a sufficient condition to achieve the control objective is derived. Theoretical analysis shows that the formation tracking error can converge to zero within a prescribed time, and remain in a small neighborhood of zero after that time. Finally, numerical simulations are given to show the effectiveness of the proposed algorithm and compare it with existing results.