The Argentine forward headed the opener after only five minutes at the Romareda, and scored a stunning solo effort for the second in the 65th.
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"It's a team effort. Everyone works hard and fights hard," Messi told Canal Plus television.
"I might be the one who scores the goals, but it is a result of everyone's work."
They moved four points clear of Real Mallorca, who moved into Spain's fourth Champions League qualification spot by crushing 10-man Atletico Madrid 4-1.
Improving Almeria were unbeaten in seven when they arrived at the Mestalla, and it took a clever turn and defence-splitting pass from Silva to set up Juan Mata for Valencia's opener in the 63rd minute.
Cash-strapped Mallorca, who have won all but one of their home games this season, took the lead through Victor after only 10 minutes against Atletico but Diego Forlan levelled for the King's Cup finalists in the 25th.
Aritz Aduriz restored Mallorca's advantage almost immediately and Atletico faded after midfielder Raul Garcia was sent off early in the second half.
"This win makes a point to all those rivals who thought off-field problems would take their toll on us," Mallorca coach Gregorio Manzano told reporters.
"Today we have proved we are a strong, ambitious team and worthy candidates for the European places."
