. . . The Supreme Court never took up the case. The Chief Justice of the Supreme Court did so in Ex parte Merryman, but he did so while sitting in as a trial judge for the United States Circuit Court for the District of Maryland, and held that the power to suspend habeas corpus lay solely with Congress. Lincoln simply ignored Taney's opinion, and that was the end of the federal judiciary's involvement with the suspension of habeas corpus.
The suspension was partially lifted with Proclamation 148, issued by President Andrew Johnson in December of 1865, which read:
Whereas by the proclamation of the President of the United States of the 15th day of September, 1863, the privilege of the writ of habeas corpus was, in certain cases therein set forth, suspended throughout the United States; and
Whereas the reasons for that suspension may be regarded as having ceased in some of the States and Territories:
Now, therefore, be it known that I, Andrew Johnson, President of the United States, do hereby proclaim and declare that the suspension aforesaid and all other proclamations and orders suspending the privilege of the writ of habeas corpus in the States and Territories of the United States are revoked and annulled, excepting as to the States of Virginia, Kentucky, Tennessee, North Carolina, South Carolina, Georgia, Florida, Alabama, Mississippi, Louisiana, Arkansas, and Texas, the District of Columbia, and the Territories of New Mexico and Arizona.
In witness whereof I have hereunto set my hand and caused the seal of the United States to be affixed.
Done at the city of Washington, this 1st day of December, A.D. 1865, and of the Independence of the United States of America the ninetieth.
ANDREW JOHNSON.
By the President:
WILLIAM H. SEWARD,
Secretary of State.
The suspension became inoperative with the end of the Civil War.
See
https://constitutioncenter.org/blog/lincoln-and-taneys-great-writ-showdown ; also
https://quod.lib.umich.edu/j/jala/2629860.0029.205/--lincoln-s-suspension-of-the-writ-of-habeas-corpus?rgn=main;view=fulltext ; and also
https://en.wikipedia.org/wiki/Habeas_Corpus_Suspension_Act_(1863)