Thomas made heavy weather of it for the duration, putting his clash with Allen in doubt, before edging a 77-74 and 76-75 (twice) decision on the cards.
The Allen fight was due to happen on the undercard of Anthony Joshua v Carlos Takam last week but was rescheduled when Thomas accepted the New York encounter.
Promoter Eddie Hearn will be happy to learn of Thomas’ victory as Allen is set to challenge for the title on the December 17 undercard of Tony Bellew v David Haye II.
Dylan Price scored a first round KO to improve to 4-0, whilst Amanda Serrano did likewise against Marilyn Hernandez and can now boast a 34-1-1 C.V.
Also on the bill, heavyweight Efe Ajagba defeated Rodney Hernandez to stay unbeaten prior to featherweight prospect Chris Colbert extending his own perfect record against previously undefeated Titus Williams.
Scores read 79-72 (twice) and 78-73 in favor of Colbert after eight completed rounds.