The 27-year-old suffered his injury late in the game at Stamford Bridge as a result of a clash with Blues defender Gary Cahill.
He was forced to leave the pitch supporting his arm in a makeshift sling.
Hammers boss Sam Allardyce confirmed after the game that O'Brien had suffered a dislocation and is likely to miss between 10 and 12 weeks.
"Joey, unfortunately, has dislocated a shoulder, which is bad news for us," said Allardyce.
"That's our third dislocated shoulder this season. I don't think I've had
three dislocated shoulders in my entire career, let alone three in one
This could see him miss 10 matches as West Ham continue their struggle against relegation from the Premier League.
West Ham's point at Stamford Bridge will help this cause although it did not prevent them dropping into the relegation zone as a result of Sunderland's 1-0 win over Stoke.
O'Brien, who has made 19 appearances for West Ham this season, was not the only injury victim on Tuesday night.
Mohamed Diame will be assessed ahead of Saturday's home match with Newcastle after suffering a bang on the knee when he fell over the advertising hoardings and had to be replaced in the first half.
Despite the injuries, Allardyce was in jovial mood afterwards as he hit back at complaints from opposite number Jose Mourinho about the visitors' tactics.
Allardyce said: "He can't take it, can he? He can't take it because we've out witted him. He just can't cope.
"I love to see Chelsea players moaning at the referee, trying to intimidate him, Jose jumping up and down saying we play crap football.
"It's brilliant when you get a result against him. Hard luck, Jose."
Allardyce lauded his players for implementing his tactics in a result he believes was on a par with the 3-0 win at Tottenham earlier in the season.
The Hammers boss added: "This one probably equals (Tottenham) because of the position we're in and the problems we've had recently.
"It was all about frustrating a team that's got world-class players and not to come here and lie down.
"Tactically we got it right in two areas particularly: one was in stopping (Eden) Hazard, Oscar and Willian and (Samuel) Eto'o scoring goals; and the other one was stopping them scoring from set plays. We did a fantastic job."