The visitors ended a six-match winless run as coach Javi Gracia claimed victory against the side he led to promotion last season, with Oriol Riera and Alejandro Arribas scoring first-half goals.
Almeria did pull one back through Fernando Soriano but they remain 19th, while Osasuna climb to 14th.
Riera put Gracia's men ahead with 19 minutes gone, turning in Marc Bertran's cross, and the away side took a two-goal lead into the interval as Arribas headed home just his second league goal of the season.
Almeria made a fight of it after the break and Soriano reduced the deficit 17 minutes from time but there was no way back for the hosts.
And Rafita's second yellow card saw him sent off in stoppage time, adding insult to injury for the losers.
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