The England striker, who is no stranger to acts of petulance himself, admonished the Portugal international for failing to control his temper
Pepe appeared to deliberately tread on his opponent midway through the second half of the first leg of the Copa del Rey quarter-final clash in the Spanish capital.
Manchester United striker Rooney, no strange to acts of on-field petulance himself, was amongst the first to admonish the Portugal international for failing to control his temper.
The England forward wrote on Twitter: "Pepe. What an idiot. Sometimes people wind u up."
When Messi then set Eric Abidal up for the winning goal moments later, Rooney added: "Haha. That goal serves pepe right."
Rooney’s international colleague Jack Wilshere was also less than impressed, adding: "Poor from Pepe!"
However, the Arsenal midfielder was extremely taken with the performance of Barcelona’s Andres Iniesta.
"Iniesta's a joke.....the best midfielder in the world! In my opinion.....the way he glides past players! Reminds me of Gazza [Paul Gascoigne]," Wilshere exclaimed.
Meanwhile, QPR’s Joey Barton was more enamoured with one of Iniesta’s midfield colleagues.
"How good is Xavi?," he asked on his Twitter account. "Head is on a swivel at all times. As good as I've ever seen that fella......"
Barton could then not resist provoking a reaction from some of his followers by adding: "[Paul] Scholes was very good but for me Xavi's better. All the biased Man U fans will go mad now, before u start u blerts, u can all **** ***!"
Tom Huddlestone, meanwhile, also brought up Scholes, as well as Steven Gerrard, during one of his musings on the game.
"Would love to see a few of these so called 'hard-men' take a scholes\stevie-G tackle in the EPL," he opined.
After recovering from Cristiano Ronaldo's early strike with goals from Carles Puyol and Abidal, Barcelona will take a 2-1 advantage into the second leg at Camp Nou next Wednesday.