Red Devils boss Roberto Martinez shuffled his pack ahead of the Nations League double header against England and Iceland, opting not to start the likes of Kevin De Bruyne, Eden Hazard and Romelu Lukaku.
The much-changed starting XI struggled against Patrice Beaumelle's side in the first half but they forged ahead early in the second courtesy of Michy Batshuayi's 19th international goal.
They were denied yet another win three minutes from time, though, with Kessie clipping home from 12 yards after Wilfried Zaha had been brought down inside the area.
Belgium was more dangerous in the opening exchanges, with Brighton and Hove Albion forward Leandro Trossard looking particularly sharp on his first international start.
Chances were few and far between during a tepid opening 45 minutes, with Batshuayi's blocked shot from Trossard's pullback the closest either side came to taking the lead.
The on-loan Crystal Palace striker was not to be denied eight minutes after the restart, slotting home from close range after his initial effort from Alexis Saelemaekers' cross had been kept out by Sylvain Gbohouo.
Substitute goalkeeper Hendrik van Crombrugge was called into action soon after, though, keeping out Nicolas Pepe's close-range effort from Zaha's cross.
Zaha was instrumental to his side's late equaliser, teasing a foul out of substitute Sebastiaan Bornauw inside the area to give Kessie the opportunity to nonchalantly lift the ball into Van Crombrugge's top-right corner and ensure the game ended all square.