The midfielder was sent off with the Hammers leading Everton 2-1, leaving his manager frustrated at what he felt was an "ordinary" tackle on Ross Barkley
Noble went from hero to villain in the space of a few minutes after putting the Hammers 2-1 ahead with a typically precise penalty in the second half.
But the 26-year-old received a second yellow card for a lunging challenge on Ross Barkley, a decision Allardyce was at pains to discuss.
"Noble’s been sent off - I’ve looked at it. Easy for me to say but Noble’s got the ball," the West Ham manager said.
"The referee has to be certain as it’s the sending off of Mark Noble, which is an ordinary tackle.
"If he’s not been carded before it doesn’t affect the game - Baines might put the free kick in but we’ve still got 2-2 with 11 men not 10."
Two Leighton Baines free kicks twice hauled Everton back level, something Allardyce found hard to digest.
He added: "Baines not only puts one [free-kick] in today, but two today. That’s three out of two home games as Pennant did the same against us against Stoke. You only expect three in the entire season."
With the scores level and West Ham reduced to 10 men, half-time substitute Romelu Lukaku capped a fine debut for Everton with the winning goal, a header, in the 85th minute.
And Allardyce praised the forward he tried to take on loan from Chelsea this summer, commenting: "Fair play to Everton, they took full advantage.
"The substitute Lukaku made a huge difference. I thought we were going to do it and get a victory, never mind a draw. We ended up losing.
"I’d been talking to Jose all summer, will he want him [Lukaku]? It was no, no, no, until Demba Ba decided to stay. Then there was a quick switch around and Everton got in there before us.
"That’s the way the cookie crumbles as they say."