While the President and Congress can't directly change an unfavorable decision, they may circumvent the decision by passing legislation that addresses the constitutional challenge while still accomplishing their goal. For example, if the Supreme Court decides corporations can contribute an unlimited amount of money to political campaigns, Congress may try to pass legislation restricting companies with foreign ownership or foreign subsidiaries from donating to prevent foreign powers from participating in the US political process.
Optionally, Congress could work with the States to ratify a constitutional amendment that effectively defeats the Court's objectives (this is a difficult and time-consuming process, however).
Congress also has the right to prevent the Supreme Court from hearing certain types of cases under their appellate jurisdiction (called jurisdiction stripping) to reduce the possibility of certain controversies being declared unconstitutional in the future. This action wouldn't prevent a specific judgment from being acted upon, but could check the judiciary and restrict them from making sweeping changes.
Because the Supreme Court has no authority to enforce its decisions, the President may ignore a decision or refuse to take action supporting it. Such was the case with many civil rights decisions made before Congress passed the Civil Rights Act of 1964 (and 1968).