September's rate dropped compared to August's 4.05 percent, but exceeded the 3 percent rate registered in September 2019, according to the agency.
In September, the National Consumer Price Index (INPC) rose 0.23 percent, slightly less than the 0.26 percent seen in the same month of 2019, Inegi said in its monthly report.
Core inflation, the benchmark for monetary policy, rose 0.32 percent in September and 3.99 percent annually, it added.
In September, the price of tomatoes fell 10.11 percent compared to the previous month, while the price of eggs dipped 3.98 percent, the agency said about the staple foods, which weigh heavily on the INPC.
In a separate report, the Banorte financial group noted inflation hovered slightly above the upper limit of the central bank of Mexico's target rate of 3 percent, with a one-point margin of tolerance up or down.
"We believe inflation has already reached its maximum of the year, maintaining our forecast that general inflation will lower in the coming months to end the year at 3.7 percent," Banorte said.
"On the positive side, goods seem to be stabilizing after strong increases since April, related to distortions from the pandemic and, to a lesser extent, the depreciation of the exchange rate," Banorte added.
Mexico closed 2019 with inflation at 2.83 percent, its lowest level since the end of 2016.