McInnes was loudly booed by Hearts fans when he emerged from the tunnel for his first match back at Tynecastle since leaving in June.
His shock departure to Rangers came just weeks after the Edinburgh side were pipped to the Scottish title by Celtic in a dramatic last-day defeat against Martin O'Neill's men.
McInnes' men initially silenced the taunts when Kevin Kelsy scored a 16th-minute opener following a mistake from Laurent Mendy.
Hearts turned the game round with goals from Claudio Braga and Calvin Miller early in the second half.
But Makhanya's 89th-minute header kept second-placed Rangers four points behind Celtic and four above third-placed Hearts.
Celtic showed their mettle as they fought back to grab a 2-2 draw at Parkhead.
Colombian striker Camilo Duran put O'Neill's team ahead in the 18th minute with his 11th goal of the season.
However, Australian forward Zac Sapsford levelled in the 28th minute with a header before defender Neil Farrugia put the visitors in front three minutes later with his first goal for the club.
Celtic piled forward in the second half and defender Liam Scales equalised with a 64th-minute header.
Hibernian moved off the bottom of the table as they drew 1-1 at St Mirren to earn Marink Reedijk his first point as manager.
Marko Ivezic put Hibernian ahead but Jason Kerr's own goal denied them a third league win this season.
Motherwell ended a six-match losing streak in a 2-2 draw at St Johnstone.
Ash Hay piled more pressure on Kilmarnock boss Neil McCann after netting a late brace to earn Dundee a 3-1 win at Dens Park.