Abubakar commended the Super Eagles despite the loss.
In a tweet, he wrote: “Well done @NGSuperEagles. We are forever proud of you. Though we didn’t make the finals, we stayed committed till the end. #TotalAFCON2019 #NGAALG.”
Algeria qualified for the final of the Africa Cup of Nations, following a 2-1 win over Nigeria on Sunday.
The Desert Foxes took the lead in the first half, thanks a William Troost-Ekong own goal.
The Super Eagles levelled in the second half, after a Video Assistant Referee (VAR) decision, with Odion Ighalo stroking home the penalty.
With the match heading into extra time, Riyad Mahrez stepped up and spanked a free-kick past Daniel Akpeyi, to send his side into the final.
They will take on Senegal in the final on Friday, July 19.
Nigeria faces Tunisia in the third-place playoff on Wednesday, July 17.