Freiburg's Max Kruse volleyed home on 50 minutes after Frankfurt defenders failed to clear the ball in their box though it was not an unusual situation for the hosts, who have repeatedly come back this season including against champions Borussia Dortmund.
Meier levelled in the 68th, turning with his back to the goal to thunder in a well-struck drive and the attacking midfielder added his fourth goal of the season five minutes later, heading in a corner.
Frankfurt, who have now won five and drawn one game in a stunning return to the top flight after a year in the second division, have 16 points and are two behind leaders Bayern Munich, who beat Werder Bremen 2-0 on Saturday.
"Obviously we had a good start but we know where we are coming from," Meier told reporters, refusing to get carried away.
"We win together and we lose together. We know what we need to do to avoid relegation. There is still a long road ahead of us."
Freiburg, who dropped to 13th on five points, were left with 10 men when substitute Karim Guede was sent off for a wild challenge reminiscent of a martial arts move in stoppage time.
Third-placed Dortmund are on 11 after crushing Borussia Monchengladbach 5-0 for their first win in three games on Saturday.
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