Jonathan died 3 December 1905 in Oregon County, Missouri.  His seventy-two year old wife, Sarah M., applied for a Widow's Pension in 1905 stating that Jonathan died 3 December 1905 and she had no former marriage. Witnesses to her testimony were Ada V Conasty and M E Durst. Sarah signed with an "X".

In June 2001, this writer contacted Veterans Affairs in Washington, DC and requested a Civil War marker for Jonathanís grave at Thayer, Missouri. A marble stone was delivered to the sexton at Thayer, but he would not place the stone at the gravesite but at a place for veterans located next to his office. Dianna Johnson contacted the Mayor to request the stone be at grave which the Mayor promised it would be done.