BAGHDAD — As the United States ends its second war in Iraq, the legacy of the first one still haunts. The memory of the first President Bush’s urging Iraqi Shiites to rebel against the government in 1991, and standing by as thousands were slaughtered, is a tragic counternarrative to the revolutions that have swept the Middle East and a torment that even now complicates relations between the countries.

In an effort to salve the long-festering wounds and to counter Iran’s influence ahead of the military drawdown, the United States ambassador, James F. Jeffrey, has offered Iraq’s Shiite leaders something they have heard very little of from Americans over the years since the United States invaded Iraq in 2003: remorse and humility.

In a move that analysts say is highly unusual for a top-level diplomat, Mr. Jeffrey has lately apologized to Iraqi politicians and tribal leaders in the Shiite-dominated south for the United States inaction during the 1991 popular uprising. Particularly galling for the Iraqis was that President George Bush publicly encouraged the revolt and then allowed American forces to stand by while it was suppressed by Saddam Hussein’s helicopter gunships and execution squads in a bloodbath that claimed tens of thousands of lives....