The Manchester United forward took to social networking site Twitter to lambast the defender as "an idiot" when he appeared to stamp on Messi's hand during Madrid's 2-1 loss in the first leg of the Copa del Rey quarterfinals.
"Pepe. What an idiot. Sometimes people wind you up," Rooney posted on Twitter.
When Messi then set Eric Abidal up for Barca's winning goal, Rooney added: "Haha. That goal serves Pepe right."
However, Guti was far from impressed at the behavior of Rooney and he believes the England striker should practice what he preaches.
"I laugh at Rooney," Guti responded on his Twitter page.
"But there are many saints in heaven, and if you want to be a saint you must lead by example. Making mistakes is human."
Guti played almost 390 games for Real Madrid before leaving for Besiktas in 2010.