Ford has agreed terms with Killie manager Jim Jefferies to keep him at the club until 2010.
The 26-year-old has signed a only short-term deal because he had surgery last summer to cure a hip problem but Jefferies assured Ford he would be rewarded with a longer contract once he had proved his fitness.
Ford initially signed for Killie as an amateur in 2004 after Jefferies picked him up from a non-league side in London and the Rugby Park manager insists the centre-half has earned his long-term deal after overcoming his injury problems.
Jefferies said: "Simon and I have agreed a deal for the rest of this season and another two on top of that.
"Simon has been unlucky because he came on a trial basis short term and when he was due to sign a longer deal he got injured.
"So then he had to go on another short-term deal to prove his fitness. It then happened to him again and it's been difficult for him.
"We've been negotiating for a couple of months now as we didn't want to wait until the end of the deal but when he was back fit.
"He's been here a couple of seasons and he's earned this deal.
"He's come through a couple of injuries and we felt it was right to give him his year and a couple more as he's not missed many games for us.
"We're confident his injuries are no longer a problem."
Meanwhile, Jefferies is waiting on the results of the scan on Allan Johnston's knee after the midfielder suffered a setback in a reserve match.
Johnston has been out since September but looked set to make his return against Motherwell tomorrow.
Jefferies added: "Allan Johnston had been coming along great and looked as though he'd be in contention but he did something in the reserve game, jarred it, and will be definitely out for the weekend.
"He's seeing a specialist and we'll know more after that."