I can’t recall an instance where Kissinger did, though there were plenty of instances where he undermined Nixon or disobeyed instructions. I am reading Dallek’s Nixon and Kissinger right now though, and will update if I find an instance.
Haldeman came closer by routinely failing to pass on Nixon’s enraged instructions to fire everybody. In his sober moments, Nixon was grateful to him for that.
The closest Nixon came to being usurped was just before his resignation. Def Sec Schlesinger and I think Haig agreed they’d block any attempt by Nixon to launch thermonuclear warfare.
EDIT: Now that I have got up to the relevant chapter of Nixon and Kissinger (p. 530). The Yom Kippur War coincided with the Saturday Night Massacre. Nixon was in no state to deal with the war, and left the handling it to Kissinger. I was prepared to think of much of it as delegation, though it was increasingly hard to: anything Nixon said during the war, Kissinger considered counterproductive.
On the night of the 24th of October, the US needed to head off Soviet threats to intervene unilaterally in the Middle East. The Washington Special Action Group, a committee for serious crisis management within the National Security Council, met, and raised the military alert to Defcon III. It worked: the Soviets, caught by surprise, stood down, and the war was over in a couple of days.
As Wikipedia mentions, citing one historian’s account:
When Kissinger asked Haig whether [Nixon] should be wakened, the White House chief of staff replied firmly ‘No.’ Haig clearly shared Kissinger’s feelings that Nixon was in no shape to make weighty decisions
Dallek’s account sounds like something Toby Ziegler would say in the West Wing, when a fairly similar scenario played out:
It was an amazing turn of events: None of the seven officials who met for over three hours until 2 A.M. had ever been elected to anything by voters. Yet they were setting policy in a dangerous international crisis. Kissinger rationalized Nixon’s absence by saying that he had never attended WSAG meetings. However, the WSAG had never confronted a crisis of this gravity before. More important, the group made decisions that should only come from the president, though Kissinger and Haig were confident that they reflected the President’s views. Others at the meeting were not so sure.