In this paper we carry out a comparative study of the daytime (7-18 LT) behavior of the near-equatorial ionospheric F region at the end of the long deep solar minimum (2009) with respect to that of the previous normal solar minimum (1995) in the Indian longitude sector using ionosonde observations of F layer parameters, radar observations of ExB drift, and the IRI-2012 (International Reference Ionosphere-2012) model. We investigate the F-2 and F-3 layer behaviors separately. The results reveal that the peak frequencies of the F layer (f(peak)), F-2 layer (f(o)F(2)), and F-3 layer (f(o)F(3)) in 2009 are consistently lower than those in 1995. Maximum difference in f(peak)/f(o)F(2)/f(o)F(3) between 2009 and 1995 observations is found in the equinoxes followed by winter and summer. The annual mean, seasonal mean, and 10day mean peak electron density (corresponding to f(peak)) in 2009 were lower than those in 1995 by as much as 34%, 46%, and 65%, respectively. Solar rotation effect is less conspicuous in 2009 than in 1995, consistent with the solar rotation signature in F-10.7. Observations also show considerable amount of equinoctial asymmetry in electron density, which is found to be closely linked with the corresponding asymmetry in the vertical ExB drift. Seasonal mean peak electron densities of the F layer (corresponding to f(peak)) and the F-2 layer (corresponding to f(o)F(2)) observed during the deep solar minimum of 2009 were smaller than those corresponding to IRI-2012 model f(o)F(2) by as much as 45% and 50%, respectively, underlining the need to incorporate the data collected during the long deep minimum in the IRI model. The unusually weak ionosphere observed in 2009 is discussed in terms of the direct effect of the low solar EUV flux in 2009 as compared to 1995 and its indirect effects on ionospheric electric field, thermospheric composition (or O/N-2 ratio), and thermospheric neutral winds.