Midfielder Dean Shiels, who now plays for Dunfermline Athletic in the Scottish Championship, had the objects hurled at him during Tuesday's 2-0 win over Falkirk.
Shiels, 32, was abused by Falkirk fans and two of the club's players, Joe McKee and Kevin O'Hara, remain suspended after being found guilty of taunting the midfielder in October over the loss of an eye.
The player had an operation to remove his right eye, which had been blind since a domestic accident when he was eight years old, eleven years ago.
A spokesman for Falkirk said: "Falkirk FC apologises unreservedly for the abhorrent behaviour of a small number of individuals.
"The club wholeheartedly condemns the abuse witnessed towards Dean Shiels in the strongest terms and will be working closely with Dunfermline Athletic FC to identify those responsible.
"Abuse towards anyone with a disability is simply unacceptable and the fact this took place with a sporting context with rivalries at play is no excuse.
"This needs to stop now. We will look to action against anyone identified from today's game and will not allow this disgraceful behaviour to be repeated."
Falkirk could face fresh disciplinary action, with the Scottish Professional Football League responsible for crowd behaviour. The governing body will review the match delegate's report before considering what action to take.
Shiels, who has 14 caps for Northern Ireland, was sent off for a stoppage-time challenge on McKee in Falkirk's 2-0 Challenge Cup win earlier in the season that sparked the two suspensions.
Striker O'Hara was given an eight-match ban and midfielder McKee was suspended for four by the Scottish Football Association following that game.
Dunfermline then had two men sent off during a league draw weeks later - Kallum Higginbotham after a challenge on McKee, who had yet to have his case heard, and Declan McManus for pushing Aaron Muirhead after the defender had fouled Shiels.
Dunfermline manager Allan Johnston told he club's website: "You never like to hear stuff like that. It's poor.
"It's great discipline he showed. The whole team showed that.
"He has had a lot to deal with, but I think the whole club have.
"I think we have dealt with it professionally, but you just have to move on."
He added: "That's why it was important to get the win as well, when stuff like that is going on in the background. It's unacceptable in this day and age.
"The most important thing was getting the win, especially against Falkirk when you see the rivalry."
In November 2008, St Mirren apologised to Shiels after one of their supporters verbally abused him regarding his disability during a match.
And Hearts also criticised their supporters after they taunted Shiels about his disability during an Edinburgh derby match while he was playing for Hibernian.
Shiels signed for Rovers in February 2009 for £50,000, scoring ten goals in 83 appearances before leaving the club in 2012.