Tosafos makes somewhat of a controversial statement. The gemara asks how we can penalize one who purchased an animal in a market of avoda zara by forcing him to mutilate the animal thereby violating tza'ar ba'alei chaim. The gemara responds by citinga pasuk in Yehoshua where he did it. Tosafos asks that since tza'ar ba'alei chaim is a Torah prohibition, a pasuk in Yehoshua is not a sufficient source to permit it (had the issur only been d'rabonon so they could have permitted it here as they did by Yehoshua, but if its d'oraysa we can't learn from Yehoshua since that may have been a special circumstance where Hashem told him to do so)? Tosafos answers that although the gemara in Yevamos 90b limits the power of the Rabbonon to uproot Torah mandates to cases where it is only uprooted passively, in truth the Rabbonon have the power to even actively uproot Torah mandates. However, this power only applies to a handful of circumstances where they have good reason to do so, such as here - דודאי שיש כח בידם לעקור היכא דנראה טעם קצת לעקור. Tosafos makes a similar point in Yevamos 88a regarding the ability to believe a woman that her husband died which contradicts the Torah mandate of two witnesses, simply because there is a good reason to assume she is telling the truth - אשה דייקא ומינסבא. Also, in Nazir 43b Tosafos explains that a kohen may be metamei for his wife even if the kiddushin to her isn't recognized by the Torah based on the rationale that she is like a meis mitzvah since everyone expects the husband to care for her. Although she is not technically a meis mitzvah, the rabbonon can a uproot a din torah when they have a compelling rationale to do so.
This concept seems very difficult to accept, especially since the gemara in Yevamos 90 elaborates about the power of the Rabbonon and concludes that they only have the ability to uproot din torah when it would result in a passive violation, not an active one. Furthermore, the source of this power is unclear.
The Chazon Ish (Even Ha'ezer 21:3) explains: Originally the Torah was given to the chachamim to decide what is deemed sufficient knowledge or testimony to verify the death of a husband and permit a woman to remarry. The default would always be two valid witnesses, but if beis din would lower the standard of evidence necessary to prove beyond doubt that the husband died, that would also be acceptable. The same is true in the realm of meis mitzvah that the rabbonon are given control to determine what circumstances would qualify as a meis mitzvah because the relatives will not care for their dead as they should. Similarly, they were given the power to decide what would qualify as tza'ar ba'alei chaim, and what would be necessary for mankind to impose a penalty for violating an issur.
According to the approach of the Chazon Ish the Rabbonon don't have the power to override din Torah actively. However, there are a handful of situations where the exact status is ambiguous and the Rabbonon have the authority to define the status. In other words, the Rabbonon are not permitting a woman who the Torah recognizes as still married, to remarry. Rather, they are given the authority to lower the standard of evidence necessary to determine that her husband is dead. Similarly, they don't have the authority to permit a kohein to become tamei, but they have the authority to expand the category of meis mitzvah. Similarly, they don't have the authority to permit tza'ar ba'alei chaim, but since even the Torah recognizes that the prohibition is relative to human need, they have the authority to decide what is considered an important need. But, in any situation where their isn't an ambiguous status, they don't have any authority to directly permit one to actively violate a din in the Torah.