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The visitors got off to the best possible start with a try from Ramiro Moyano just seconds after kick-off.
But Thomas scored one try after 25 minutes and another eight minutes into the second half after superb work from centre Gael Fickou.
Hooker Guirado sealed victory for the home side with a try nine minutes from time after he capitalized on a handling error just metres from the line.
Nicolas Sanchez scored two penalties and a conversion for the Pumas and Baptiste Serin kicked 13 points for 'les Bleus' in a scrappy match.
Both sides were desperate for a win after disappointing results last week, with the French losing in stoppage time to South Africa and Argentina struggling to a 28-17 defeat by Ireland.
But although the Pumas started well they were overpowered by a French team who were too strong and too robust.
The match was an early preview of what is to come in the 2019 World Cup, with both sides drawn together in a pool with England, USA and Tonga.
The win in Lille was France's first since March, when they beat England in the Six Nations. It also extended Argentina's losing run to four matches.
The South Americans travel to Murrayfield to play Scotland next Saturday, while France take on Fiji in Paris.