The Arsenal forward, whose participation for the Under-21s has been a bone of contention for Arsene Wenger in the past, was making only his second appearance since returning from a lower back injury.
Cool head: Theo Walcott goes round keeper Kristijan Naumovski to set up England's first goal
And his latest injury, albeit a minor one, may cause a small amount of further unrest at the Emirates, although Walcott's potential inclusion for the senior squad's clash against Belarus next Wednesday is now very much in doubt.
A 20,074 crowd at the Ricoh Arena were treated to a thrilling European Championship qualifier as England were made to work hard for their three Group Nine points.
Kieran Gibbs and Micah Richards put England in control before Muarem Muarem made it 2-1 at the interval.
But a blistering start to the second half saw Macedonia make it 3-3 in the space of six minutes through Agim Ibraimi and a Gibbs own goal, with Andy Carroll netting for England.
But, despite a fair share of nerves, Stuart Pearce's charges triumphed courtesy of another from Carroll and a brace from substitute Zavon Hines - on his debut.
Clear head: Micah Richards directs his effort into the roof of the net
England's European Championship final defeat in Sweden over the summer marked the end of a two-year cycle for head coach Pearce, with just four players starting at the Ricoh from the side that lost 4-0 to Germany.
Both sides made a solid start to the encounter with Ibraimi the first to test goalkeeper Scott Loach with a stinging free-kick that the Watford man safely parried away for a corner.
England started to grab a foothold on the game somewhat as the first quarter wore on but Macedonia were more than willing to commit men forward themselves.
The midfield quartet of Jack Wilshere, Danny Rose, Jack Rodwell and Tom Cleverley looked more than at ease as they worked the ball around - and the latter two combined for England's opener after 22 minutes.
Cleverley did extremely well to keep Rodwell's crossfield pass in play as he hugged the touchline, before playing a through-ball for Walcott.
All white: England's Kieran Gibbs (right) celebrates with Theo Walcott (left) after scoring the opening goal
And the England number 10 lofted a perfect ball to the back post where Gibbs was on hand to head home.
The young lions only had to wait eight minutes for a second. The classy Wilshere floated a corner to the near post for Michael Mancienne to flick on - and Richards nodded past Kristijan Naumovski.
Loach did well to save from Ibraimi for a second time before Macedonia grabbed a lifeline in the 42nd minute.
Muarem fired in a low free-kick from the left side of the penalty area and, despite the best efforts of Betim Aliju, the ball appeared to go untouched before beating Loach.
West Ham youngster Hines came on at half-time for the injured Walcott.
In the 52nd minute Mancienne slipped before making a complete hash of his attempted interception, allowing the lively Ibraimi to level matters.
England were back in front just two minutes later, though, as Carroll flicked Gibbs' near-post cross over Naumovski.
Thebreathtaking second half continued when the visitors made it 3-3 in the58th minute. Ibraimi whipped a vicious corner into the penalty area andas the ball was knocked goalwards, Gibbs - who was standing on thegoalline - put it into his own net.
Pearce must surely have been hugely alarmed at the kamikaze second-half performance from his side.
Nevertheless, his charges regained their lead in the 67th minute courtesy of Hines.
The 20-year-old latched onto Cleverley's through-ball before putting his finish between the legs of Naumovski, before Carroll and Hines put the gloss on the scoreline in the closing stages.