Merhi will take Kobayashi's place for FP1, which will be the 23-year-old's first run in F1 machinery.
"I am delighted to be taking part in my first ever Formula One free practice session and I want to thank Caterham F1 Team for this opportunity - it's something I've wanted for a very long time," Merhi said.
"I've been working very closely with the team during the last few weeks and I feel ready for this opportunity; Friday is going to be a very special day for me and one I will never forget."
Merhi makes the step up to F1 racing having taken two victories so far - and a podium in the Monza season opener - in this year's Formula Renault 3.5 championship. He previously stormed to the 2011 European Formula Three title, before spending two seasons driving for Mercedes-backed teams in Germany's DTM touring car series.
"What a year it's been so far," he added. "Last Christmas I didn't really know if I was going to carry on racing and now I'm about to drive a Formula One car! I'm definitely going to make the most out of this weekend in Italy."
Kobayashi, meanwhile, returns for the Formula 1 Gran Premio d'Italia 2014 after sitting out the previous round at Spa-Francorchamps to make way for three-time Le Mans winner Andre Lotterer.
"I am working for Caterham F1 Team and I always respect team decisions," Kobayashi said. "Now I am back in the car and looking forward to going racing again!
"We have worked hard as a team and added performance to the car as well as bringing new updates since I last drove in Hungary before the summer break, so I'm looking forward to feeling the updates on track here in Monza."