The drivers were running one-two halfway through Saturday's second leg and, in a move that made the outcome effectively a foregone conclusion, the team decided they should take no risks.
Citroen principal Yves Matton said he had spoken to both men to ensure eight-times world champion Loeb of France takes his 70th race win.
"Sebastien almost went off (on stage nine) and we can't afford to throw away a possible one-two which would be a great result for both championships," Matton told the world rally website.
"It's a bit hard on Mikko after what happened in Portugal but I hope he'll be able to stand on the top step of the podium again with us very soon."
Hirvonen was stripped of his win in Portugal, which would have seen him take Loeb's championship lead, after stewards found Citroen had fitted his car with a clutch that did not conform to the rules.
With two stages of the second day remaining in Argentina,
Loeb was 7.7 seconds ahead of Hirvonen. They had been separated earlier in the day by just 2.1 seconds after ending the first leg just 1/10th apart.
Spain's Dani Sordo, driving a works team Ford as a stand-in for the injured Jari-Matti Latvala, was third and a massive one minute 29.8 seconds adrift of Hirvonen.
Latvala was forced to miss the fifth round of the season after breaking his left collarbone in a cross-country skiing accident while training in his native Finland. He is expected back for Greece next month.