There is provided a pacemaker system with capture verification and threshold testing, in which the pacemaker adjusts the post-stim pulse portion of a triphasic pulse to minimize polarization, and waits after each change in delivered pace pulses for a stabilization interval, in order to enhance capture verification. The threshold test utilizes a pace pulse pair, comprising a prior search pulse which is varied during the test, and the regular pacing pulse which is above threshold. When delivery of the pulse pairs is initiated, the search pulse is adjusted to optimize polarization, and the pacemaker waits for a predetermined stabilization period of time in order to allow for minimum polarization and to optimize capture detection. The search pulse is increased incrementally in output value toward threshold, and following each such increase the pacemaker waits for a stabilization interval. The pacemaker detects when capture is achieved by the search pulse, thereby providing an indication of threshold. The polarization minimization feature involves scanning the post-stim duration to find the optimal duration. The polarization minimization also enables detection of repolarization signals, and consequent pacemaker functions such as AAIR pacing and suppression of atrial tachycardia.