Steve Nzonzi pulled a goal back but Wheater's first Premier League goals for more than three years halted Blackburn's mini-revival and gave Owen Coyle's team fresh hope of avoiding the drop as they climbed out of the bottom three.
Muamba's name was chanted at various stages of the game, including both sets of fans before kick-off, while his name rang out after a frenzied finish failed to bring Blackburn an equaliser.
The 23-year-old midfielder remains seriously ill after suffering a cardiac arrest during the FA Cup tie against Tottenham at White Hart Lane last weekend. His heart stopped for 78 minutes as doctors battled on the pitch and in hospital to keep him alive.
Bolton and Blackburn players warmed up in shirts with Muamba 6 on the back, while fans in one stand held up cards spelling out the player's name when the teams ran out on to the pitch.
Manager Coyle called for his team to follow Muamba's fighting spirit, and winger Martin Petrov set the tone with an early effort from 30 yards that Paul Robinson saved with difficulty.
But the home side were lucky not to fall behind after 23 minutes.
Junior Hoillet burst into the Bolton penalty area to be sent tumbling by a combined challenge from Gretar Steinsson and Mark Davies but referee Andre Mariner, who had a decent view, waved away penalty claims.
Rovers sensed that they were in with a chance of recording a third successive victory when Tim Ream had to make a vital interception to prevent Ayegbeni Yakubu sliding in for the opening goal at the far post.
But Ream's centre-half partner Wheater changed that perception almost immediately when he headed Bolton in front thanks in part to a woeful defensive header from Nzonzi.
The home crowd celebrated by singing Muamba's name, and that in turn seemed to strengthen Bolton's resolve to claim a much-needed victory as Darren Prately headed just over the Rovers bar.
Yakubu, whose 14 goals have steered Blackburn away from the depths of the league table, missed a chance to equalise when he stabbed a shot wide from 10 yards to add to the visitors' discomfort.
But it was mostly Bolton's possession, and with 35 minutes gone Bolton increased their lead after Robinson was forced to concede another corner in saving Petrov's fierce angled shot from the left.
When Ryo Miyaichi's corner arrived in the crowded area, Wheater escaped his marker Scott Dann and propelled the firmest of headers beyond Robinson's reach to put the home side in command.
Dann attempted to make amends as the first half came to a close, diving low for a far-post header that went into the side-netting but Blackburn clearly had some leeway to make up.
Their players came out early for the second half and halved Bolton's lead after 56 minutes when Nzonzi made up for his earlier lapse by heading home Morten Gamst Pedersen's long throw to the near post.
Victory was a timely lift for Bolton, who will go ahead on Tuesday night with the replay of their FA Cup quarter-final, which was abandoned within minutes of Muamba's collapse.
Source: AFP
Source: AFP