The Aston Martin driver secured fourth place in the drivers' championship with a seventh-place finish at the Yas Marina Circuit but was noted by the stewards for an incident following his second pitstop in the season finale.
As he rejoined the circuit, with Hamilton's Mercedes closing behind, Alonso moved to the right-hand side of the road on the approach to the Turn 5 left-hand hairpin, then appeared to lift off the throttle.
This caught Hamilton off-guard, with the seven-time world champion reporting to his team that Alonso had brake-tested him, however the stewards decided not to take any action after considering a charge of driving erratically.
Hamilton immediately passed Alonso using DRS, but the Spaniard retook the place and eventually finished two positions ahead of Hamilton after the Brit failed to make his final lap move on Yuki Tsunoda's AlphaTauri stick.
Speaking after the race, Alonso explained that he had slowed with the intention of allowing Hamilton through so he could instead gain DRS on the long drag towards Turn 6.
When asked for his response to Hamilton's brake test allegation, Alonso replied: "Lewis is obviously very clever and understands the sport really good and has a lot of experience but I have more."
Asked to clarify whether he was surprised by Hamilton's comment, Alonso added: "Yes and no.
"We did the same in Canada in 2012, so 11 years after that episode, we tried to give the DRS to the other guy, braking for Turn 5 but in both cases, I won so it is okay."
Alonso clarified that Aston Martin "need a lot more pace to overtake, we were a little bit slow on the straights", which he said had been "our weakness all throughout the season".
This was compounded by discovering that tyre wear was higher than expected.
"By lap 16 or something like that we made the first stop and we knew that the race was long from that point," Alonso said. "But at the end, the pace was only good for seventh or eighth.
"As I said yesterday the lap in qualifying was very good for the position, but the pace was a concern. That’s what we saw today.
"We were just enough to beat AlphaTauri but that is not enough."
Lance Stroll also scored a point in 10th as Aston Martin concluded the season fifth in the constructors' table.
