Perhaps from the old practice of knocking under the table with the knuckles, when conquered. Compareknuckle under

knockunder (third-person singular simple presentknocks under,present participleknocking under,simple past and past participleknocked under)

1. (intransitive,dated) Toacknowledge oneselfconquered; tosubmit, toyield.
   • 1823, [James Fenimore Cooper], chapter XIV, inThe Pioneers, or The Sources of the Susquehanna; […], volume II, New York, N.Y.:Charles Wiley; […],→OCLC,page209:

     I pull the second best trigger in this county. Iknock under to Natty Bumppo there, sin' he shot the pigeon.

   • 1852,William Makepeace Thackeray, “I Come to an End of My Battles and Bruises”, inThe History of Henry Esmond, Esq.[…], volume III, London:[…]Smith, Elder, & Company, […],→OCLC,page 4:

     When he heard this news of Beatrix's engagement, Colonel Eſmondknocked under to his fate, and reſolved to ſurrender his ſword, that could win him nothing now he cared for;[…]

2. (intransitive,dated,slang) To die.