var re=/\[[a-zA-Z0-9\s]+\]\(@\d+\.\d+\)/

var md = 'bla bla bla [rel link 1](@2.1) bla bla [link 2](@3.4)'
var matches;
var firstMatch;
var matchIndex;
var remaining = md;
var bits = [];
var beforeMatch;
var afterMatch;

do {

  matches = re.exec(remaining);
  if(! matches) {
    break;
  }
  firstMatch = matches[0];
  matchIndex = remaining.indexOf(firstMatch);
  beforeMatch = remaining.slice(0, matchIndex);
  remaining = remaining.slice(firstMatch.length + matchIndex);
  bits.push({
    md: beforeMatch
  });
  bits.push({
    link: firstMatch
  });

} while(1)

console.log(bits);