The Spaniard, starting last after being handed 40 positions in grid penalties, took advantage of the chaos in front of him to climb up to fifth position before the halfway point of the race.
From there, however, the Spaniard was unable to keep his rivals behind him and lost places and fell to a finishing position of ninth.
With all the leading cars hitting problems at various points, Alonso believes that McLaren should have been in a position to win.
“It was a race that in normal circumstances we should have won,” said Alonso.
“Because I was with (race winner Daniel) Ricciardo when the first safety car came out.
“Hamilton lost his headrest, Vettel was penalised, both the Force Indias were out, Kimi retired…
“So you are automatically in the top two or three, so we should have fought for victory, but unfortunately we are not in that position,” he added.
Alonso, who had failed to score a point before Baku, admitted that all the incidents in front had benefitted him.
He also conceded that he had never expected to score points Baku, where the long straight hurt McLaren due to its lack of engine power.
“In our case everything worked in our favour,” he added.
“It's one of those days when you win places by elimination for free, but then it's a shame we can't keep it because of our current deficiencies.
“Scoring two points in Baku was impossible to think before coming here, so it's welcome.”
Alonso finished over 32 seconds in front of team-mate Stoffel Vandoorne in 12th.