"If defeating an insurgent formation produces popular resentment, the victory is hollow and unsustainable," McChrystal said at his confirmation hearing.
"This is a critical point. It may be the critical point. This is a struggle for the support of the Afghan people.
"Our willingness to operate in ways that minimize casualties or damage -- even when doing so makes our task more difficult -- is essential to our credibility."
Civilian casualties -- often from US air power -- have caused mounting popular outrage in Afghanistan and friction with the Kabul government, with US and Western officials worried about handing propaganda victories to their Taliban foes.
President Hamid Karzai has demanded a halt in air strikes after one of the deadliest such incidents of the war in Bala Buluk, where his government says 140 civilians died earlier this month.
McChrystal, named to replace General David McKiernan as the top commander in Afghanistan, vowed to make protecting civilian lives a top priority.
Success in the conflict against insurgents should be measured not in the number of enemy killed but in "the number of Afghans shielded from violence," he said.
McChrystal, who met with a mostly friendly reception from members of the Senate Armed Services Committee, is due to take over the helm at a pivotal moment in the Afghan war after Obama unveiled a new strategy and ordered more than 21,000 additional troops to bolster the US force.
As a former special operations commander, McChrystal's elite troops carried out manhunts in Iraq that won him praise but human rights groups say his special forces lacked restraint in their interrogations of detainees.
McChrystal did not face a tough grilling from senators over the issue, but acknowledged he had misgivings about harsh interrogation techniques that were approved by then-secretary of defense Donald Rumsfeld.
Asked if he had been "uncomfortable" with the use of dogs, stress positions, sleep deprivation and other methods in Iraq that were permitted by George W. Bush's administration, McChrystal said: "I was."
He said his troops gradually reduced the use of the harsh methods over time, even though his superiors had approved such methods.
The Obama administration has rejected torture or "enhanced" interrogation techniques that were employed during Bush's presidency.
McChrystal said that as commander in Afghanistan he would "strictly enforce the highest standards of detainee treatment consistent with international and US law."
Echoing comments by other top officials, the general said combat casualties would probably rise as more US forces deploy to the volatile south.
"Success will not be quick or easy. Casualties will likely increase. We will make mistakes," he said.
When asked if the war could be won, McChrystal said: "I believe it is winnable, but I don't think it will be easily winnable."
McChrystal also faced questions about his handling of the "friendly fire" death in Afghanistan in 2004 of Army Ranger and former National Football League star Pat Tillman.
McChrystal approved the awarding of a Silver Star to Tillman but the next day sent a memo to senior officers to warn the White House that it was likely the former football player had been killed by friendly fire.
The general told senators he regretted the episode and had failed to carefully read the citation for the award but that he and his colleagues did not intentionally mislead Tillman's family.
"We failed the family. I was part of that and I apologize for that," he said.
------------------------------------------------------------------------------------------------