It’s well known that Avraham kept the entire Torah which clearly prohibits human sacrifice, but once HaShem tells him to sacrifice Yitzchak he was willing to break that law. So obviously HaShem can suspend the Torah’s laws. Is there any other case where HaShem asks a Navi to do something contrary to the Torah?
Hashem tells Yechezkel that his wife is going to die, and that he specifically shouldn't observe several of the practices of aveilus (Yechezkel 24:16-17). It's a machlokes whether the first day's aveilus is Min Hatorah or Miderabanan (Shulchan Aruch Yoreh Deah 398), but either way these laws are part of Torah.
Eliyahu at Har Carmel. Standard halachic opinion is that sacrifices away from the Temple were forbidden. So Eliyahu was either directly told to break this, or decided on his own and that decision was then endorsed by the resulting fire.
Rambam seems to understand the first way. See the Hilchos Yesodei HaTora 9:3 where he says that Eliyahu was acting under the command of Hashem to bring a sacrifice on a private altar while the Temple was in existence even though this was ordinarily forbidden.
Similarly, a prophet who violated his own prophetic instructions, and one who refrains from prophesying, are liable for death at the hand of God, since concerning the three of them, it is said, "I will seek [retribution] from him."
When a prophet - who has already proven himself to be a prophet - instructs us to violate one of the mitzvot of the Torah or many mitzvot, whether they be of a severe or light nature, for a limited amount of time, it is a mitzvah to listen to him.
The Sages of the early generation taught as part of the oral tradition: If a prophet tells you to violate the precepts of the Torah as Elijah did on Mount Carmel, listen to him with regard to all things except the worship of false gods. This applies when his command is temporary in nature.
For example, on Mount Carmel, Elijah offered a sacrifice outside [the Temple's premises], even though Jerusalem was chosen for such [service], and one who offers a sacrifice outside [the Temple's premises] is liable for karet. Since he was [already established as] a prophet, it was a mitzvah to listen to him. The commandment, "Listen to him," applies in these circumstances as well.
If they would have asked Elijah: How can we violate the Torah's command [Deuteronomy 12:13]: "[Be careful...] lest you offer your burnt offerings everywhere"?, he would have told them: We should not say anything, but anyone who offers a sacrifice outside [the Temple premises] is liable for karet, as Moses said. [The present instance,] however, [is an exception]. I am offering a sacrifice today outside [the Temple] at God's command in order to disprove the prophets of Ba'al.
Similarly, if any [other] prophet commands us to transgress for a limited time, it is a mitzvah to listen to him. If, however, he says that the mitzvah has been nullified forever, he is liable for execution by strangulation, for the Torah has told us: "[It is] for us and our children forever."
The Talmud (Chullin 5a) states:
לימא מסייע ליה והעורבים מביאים לו לחם ובשר בבקר ולחם ובשר בערב ואמר רב יהודה אמר רב מבי טבחי דאחאב על פי הדבור שאני
Can we say that the following supports his [R. ‘Anan's] view? It is written: And the ravens brought him bread and flesh in the morning, and bread and flesh in the evening, and Rab Judah explained this in the name of Rab that [the ravens brought the flesh] from Ahab's slaughterers! — Being a Divine command it is different.
R. Anan's view appears earlier (4b):
דאמר רב ענן אמר שמואל ישראל מומר לעבודת כוכבים מותר לאכול משחיטתו
R. ‘Anan, who said in the name of Samuel: In the case of an Israelite who is an apostate in respect of idolatry, we may eat of his slaughtering.
Thus, the Talmud attempts to support R. Anan's view by noting that Elijah seemed to have acted in accordance with it, by eating meat slaughtered by Ahab's slaughterers. The Talmud rejects this support, though, because it's possible that R. Anan is really wrong, and the meat in that case would actually have been forbidden, but Elijah was able to eat it anyway because God told him to.
According to this rejection, we have here an example of God telling (or at least allowing) a prophet to break a law.